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Caperta AD, Fernandes I, Conceição SIR, Marques I, Róis AS, Paulo OS. Ovule Transcriptome Analysis Discloses Deregulation of Genes and Pathways in Sexual and Apomictic Limonium Species (Plumbaginaceae). Genes (Basel) 2023; 14:genes14040901. [PMID: 37107659 PMCID: PMC10137852 DOI: 10.3390/genes14040901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The genus Limonium Mill. (sea lavenders) includes species with sexual and apomixis reproductive strategies, although the genes involved in these processes are unknown. To explore the mechanisms beyond these reproduction modes, transcriptome profiling of sexual, male sterile, and facultative apomictic species was carried out using ovules from different developmental stages. In total, 15,166 unigenes were found to be differentially expressed with apomictic vs. sexual reproduction, of which 4275 were uniquely annotated using an Arabidopsis thaliana database, with different regulations according to each stage and/or species compared. Gene ontology (GO) enrichment analysis indicated that genes related to tubulin, actin, the ubiquitin degradation process, reactive oxygen species scavenging, hormone signaling such as the ethylene signaling pathway and gibberellic acid-dependent signal, and transcription factors were found among differentially expressed genes (DEGs) between apomictic and sexual plants. We found that 24% of uniquely annotated DEGs were likely to be implicated in flower development, male sterility, pollen formation, pollen-stigma interactions, and pollen tube formation. The present study identifies candidate genes that are highly associated with distinct reproductive modes and sheds light on the molecular mechanisms of apomixis expression in Limonium sp.
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Affiliation(s)
- Ana D Caperta
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Isabel Fernandes
- cE3c-Centre for Ecology, Evolution and Environmental Changes, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sofia I R Conceição
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- LASIGE Computer Science and Engineering Research Centre, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Isabel Marques
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Forest Research Centre (CEF), Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Ana S Róis
- Linking Landscape, Environment, Agriculture and Food (LEAF), Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- School of Psychology and Life Sciences, Universidade Lusófona de Humanidades e Tecnologias (ULHT), Campo Grande 376, 1749-024 Lisboa, Portugal
| | - Octávio S Paulo
- cE3c-Centre for Ecology, Evolution and Environmental Changes, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Marabuto E, Nunes MS, Martins R, Mendes R, Moreira-Pinhal TC, Raimundo J, Seabra SG, Paulo OS. Integrative analysis reveals the divergence and speciation between sister Sooty Copper butterflies Lycaena bleusei and L. tityrus. Mol Phylogenet Evol 2023; 180:107699. [PMID: 36621583 DOI: 10.1016/j.ympev.2022.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/07/2023]
Abstract
The comparison of closely related taxa is cornerstone in biology, as understanding mechanisms leading up to differentiation in relation to extant shared characters are powerful tools in interpreting the evolutionary process. Hotspots of biodiversity such as the west-Mediterranean, where many lineages meet are ideal grounds to study these processes. We set to explore the interesting example of Sooty Copper butterflies: widespread Eurasian Lycaena tityrus (Poda, 1761) comes into contact in Iberia with closely related and local endemic, L. bleusei (Oberthür, 1884), which hasn't always been considered a distinct species. An integrative analysis was designed, combining the use of extensive molecular data (five genes), geometric morphometrics analyses, verified and up-to-date distribution data, and environmental niche modelling, aimed at deciphering their true relationship, their placement within European Lycaena and trace their evolutionary history. We revealed several levels of differentiation: L. bleusei and L. tityrus appear to be reciprocally monophyletic independent gene-pools, distinct in all genes analysed, having mutually diverged 4.8 Ma ago. L. tityrus but not L. bleusei, further displays a genetic structure compatible with several glacial refugia, where populations assignable to infraspecific taxa surface. Conversely, L. bleusei shows a loss in mtDNA diversity in relation to nuDNA. Morphological analyses differentiate both species according to size and shape but also discriminate strong seasonal and sexual traits and a geographical phenotype segregation in L. tityrus. Finally, updated distribution and its modelling for current and glacial timeframes reveal both species respond differently to environmental variables, defining a mostly parapatric distribution and an overlapping belt where sympatry was recovered. During the last glacial maximum, a wider expansion in L. bleusei distribution explains current isolated populations. Our study highlights the importance of gathering several lines of evidence when deciphering the relationships between closely related populations in the fringe of cryptic species realm.
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Affiliation(s)
- Eduardo Marabuto
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Current affiliation: Leibniz Institute fir the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn & Senckenberg Natural History Collections, Dresden, Germany.
| | - Miguel S Nunes
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Renata Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Current affiliation: Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Golm, 14476 Potsdam, Germany
| | - Raquel Mendes
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Tatiana C Moreira-Pinhal
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; Associação BioLiving, Rua do Outeiro, 3850-635 Frossos, Albergaria-a-Velha, Portugal
| | - João Raimundo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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Marques I, Fernandes I, Paulo OS, Batista D, Lidon FC, Partelli F, DaMatta FM, Ribeiro-Barros AI, Ramalho JC. Overexpression of Water-Responsive Genes Promoted by Elevated CO 2 Reduces ROS and Enhances Drought Tolerance in Coffea Species. Int J Mol Sci 2023; 24:ijms24043210. [PMID: 36834624 PMCID: PMC9966387 DOI: 10.3390/ijms24043210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023] Open
Abstract
Drought is a major constraint to plant growth and productivity worldwide and will aggravate as water availability becomes scarcer. Although elevated air [CO2] might mitigate some of these effects in plants, the mechanisms underlying the involved responses are poorly understood in woody economically important crops such as Coffea. This study analyzed transcriptome changes in Coffea canephora cv. CL153 and C. arabica cv. Icatu exposed to moderate (MWD) or severe water deficits (SWD) and grown under ambient (aCO2) or elevated (eCO2) air [CO2]. We found that changes in expression levels and regulatory pathways were barely affected by MWD, while the SWD condition led to a down-regulation of most differentially expressed genes (DEGs). eCO2 attenuated the impacts of drought in the transcripts of both genotypes but mostly in Icatu, in agreement with physiological and metabolic studies. A predominance of protective and reactive oxygen species (ROS)-scavenging-related genes, directly or indirectly associated with ABA signaling pathways, was found in Coffea responses, including genes involved in water deprivation and desiccation, such as protein phosphatases in Icatu, and aspartic proteases and dehydrins in CL153, whose expression was validated by qRT-PCR. The existence of a complex post-transcriptional regulatory mechanism appears to occur in Coffea explaining some apparent discrepancies between transcriptomic, proteomic, and physiological data in these genotypes.
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Affiliation(s)
- Isabel Marques
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Isabel Fernandes
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Octávio S. Paulo
- cE3c—Center for Ecology, Evolution and Environmental Changes and CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Dora Batista
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
| | - Fábio Partelli
- Centro Universitário do Norte do Espírito Santo (CEUNES), Departmento Ciências Agrárias e Biológicas (DCAB), Universidade Federal Espírito Santo (UFES), São Mateus 29932-540, ES, Brazil
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa 36570-900, MG, Brazil
| | - Ana I. Ribeiro-Barros
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
- Correspondence: (A.I.R.-B.); or (J.C.R.)
| | - José C. Ramalho
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
- Correspondence: (A.I.R.-B.); or (J.C.R.)
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Mendes R, Nunes VL, Marabuto E, Costa GJ, Silva SE, Paulo OS, Simões PC. Testing drivers of acoustic divergence in cicadas (Cicadidae: Tettigettalna). J Evol Biol 2023; 36:461-479. [PMID: 36514855 PMCID: PMC10107868 DOI: 10.1111/jeb.14133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022]
Abstract
Divergence in acoustic signals may have a crucial role in the speciation process of animals that rely on sound for intra-specific recognition and mate attraction. The acoustic adaptation hypothesis (AAH) postulates that signals should diverge according to the physical properties of the signalling environment. To be efficient, signals should maximize transmission and decrease degradation. To test which drivers of divergence exert the most influence in a speciose group of insects, we used a phylogenetic approach to the evolution of acoustic signals in the cicada genus Tettigettalna, investigating the relationship between acoustic traits (and their mode of evolution) and body size, climate and micro-/macro-habitat usage. Different traits showed different evolutionary paths. While acoustic divergence was generally independent of phylogenetic history, some temporal variables' divergence was associated with genetic drift. We found support for ecological adaptation at the temporal but not the spectral level. Temporal patterns are correlated with micro- and macro-habitat usage and temperature stochasticity in ways that run against the AAH predictions, degrading signals more easily. These traits are likely to have evolved as an anti-predator strategy in conspicuous environments and low-density populations. Our results support a role of ecological selection, not excluding a likely role of sexual selection in the evolution of Tettigettalna calling songs, which should be further investigated in an integrative approach.
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Affiliation(s)
- Raquel Mendes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Vera L Nunes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Gonçalo J Costa
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Sara E Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Paula C Simões
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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Pina-Martins F, Caperta AD, Conceição SIR, Nunes VL, Marques I, Paulo OS. A first look at sea-lavenders genomics - can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex? BMC Plant Biol 2023; 23:34. [PMID: 36642719 PMCID: PMC9841708 DOI: 10.1186/s12870-022-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Sea-lavenders (Limonium Mill., Plumbaginaceae) are a cosmopolitan group of diploid and polyploid plants often adapted to extreme saline environments, with a mostly Tethyan distribution, occurring in the Mediterranean, Irano-Turanian, Euro-Siberian and in the New World. The halophylic Limonium vulgare polyploid complex in particular, presents a large distribution throughout extreme salt-marsh habitats and shows little morphological but high taximetric variation, frequently blurring species delimitation. In this work we pursue three main goals: assert whether SNP data from polyploid individuals has the resolution to distinguish the seven sampled species, to better understand how genetically structured Limonium vulgare is, and attempt to identify specific molecular mechanisms for the differentiation between L. maritimum and L. vulgare. For this purpose, 95 individuals were genotyped using Genotyping by Sequencing (GBS), which were assembled as two independent datasets using IPYRAD. All analyses performed downstream of assembly were fully automated. Phylogenetic inference, PCA, and admixture plots were used to infer answers to the study's main goals. RESULTS Close to 10,000 SNPs were obtained for each dataset. Phylogenetic analyses reveal that polyploid data can be used to infer species relationships. Population structure analyses suggest a genetically structured L. vulgare. A set of 34 SNPs were found to be fully segregated between L. vulgare and L. maritimum, two of which are potentially linked to proteins that might be involved in the speciation process. CONCLUSION Despite polyploid data analyses shortcomings, GBS generated SNPs have the resolution to discern all seven included species. Limonium vulgare revealed pronounced genetic structure along a geographical north-south cline. L. maritimum always appears as a distinct genetic entity. Segregated SNPs between L. vulgare and L. maritimum indicate salinity response and morphological trait control genes as potentially interesting to follow up for studying these species' divergence process.
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Affiliation(s)
- Francisco Pina-Martins
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Ana D Caperta
- LEAF-Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Sofia I R Conceição
- LEAF-Linking Landscape, Environment, Agriculture and Food, Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
- LASIGE Computer Science and Engineering Research Centre, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Vera L Nunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Isabel Marques
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
- Forest Research Centre (CEF) & Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017, Lisbon, Portugal
| | - Octávio S Paulo
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
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Fernandes I, Paulo OS, Marques I, Sarjkar I, Sen A, Graça I, Pawlowski K, Ramalho JC, Ribeiro-Barros AI. Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome. Plants (Basel) 2022; 11:2942. [PMID: 36365395 PMCID: PMC9658546 DOI: 10.3390/plants11212942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Climate change and the accelerated rate of population growth are imposing a progressive degradation of natural ecosystems worldwide. In this context, the use of pioneer trees represents a powerful approach to reverse the situation. Among others, N2-fixing actinorhizal trees constitute important elements of plant communities and have been successfully used in land reclamation at a global scale. In this study, we have analyzed the transcriptome of the photosynthetic organs of Casuarina glauca (branchlets) to unravel the molecular mechanisms underlying salt stress tolerance. For that, C. glauca plants supplied either with chemical nitrogen (KNO3+) or nodulated by Frankia (NOD+) were exposed to a gradient of salt concentrations (200, 400, and 600 mM NaCl) and RNA-Seq was performed. An average of ca. 25 million clean reads was obtained for each group of plants, corresponding to 86,202 unigenes. The patterns of differentially expressed genes (DEGs) clearly separate two groups: (i) control- and 200 mM NaCl-treated plants, and (ii) 400 and 600 mM NaCl-treated plants. Additionally, although the number of total transcripts was relatively high in both plant groups, the percentage of significant DEGs was very low, ranging from 6 (200 mM NaCl/NOD+) to 314 (600 mM NaCl/KNO3+), mostly involving down-regulation. The vast majority of up-regulated genes was related to regulatory processes, reinforcing the hypothesis that some ecotypes of C. glauca have a strong stress-responsive system with an extensive set of constitutive defense mechanisms, complemented by a tight mechanism of transcriptional and post-transcriptional regulation. The results suggest that the robustness of the stress response system in C. glauca is regulated by a limited number of genes that tightly regulate detoxification and protein/enzyme stability, highlighting the complexity of the molecular interactions leading to salinity tolerance in this species.
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Affiliation(s)
- Isabel Fernandes
- Computational Biology and Population Genomics Group, cE3c–Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, cE3c–Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Isabel Marques
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Indrani Sarjkar
- Bioinformatics Facility, University of North Bengal, Siliguri 734013, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Siliguri 734013, India
| | - Inês Graça
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - José C. Ramalho
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal
| | - Ana I. Ribeiro-Barros
- Forest Research Centre (CEF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal
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Costa GJ, Nunes VL, Marabuto E, Mendes R, Silva DN, Pons P, Bas JM, Hertach T, Paulo OS, Simões PC. The effect of the Messinian salinity crisis on the early diversification of the
Tettigettalna
cicadas. ZOOL SCR 2022. [DOI: 10.1111/zsc.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gonçalo J. Costa
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Vera L. Nunes
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Raquel Mendes
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Diogo N. Silva
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Pere Pons
- Departament de Ciències Ambientals Universitat de Girona Girona Catalonia Spain
| | - Josep M. Bas
- Departament de Ciències Ambientals Universitat de Girona Girona Catalonia Spain
| | - Thomas Hertach
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Natural History Museum of Bern Bern Switzerland
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Paula C. Simões
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
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Rodrigues ASB, Silva DN, Várzea V, Paulo OS, Batista D. Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History. Phytopathology 2022; 112:1998-2011. [PMID: 35322716 DOI: 10.1094/phyto-09-21-0376-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The devastating disease coffee leaf rust, caused by Hemileia vastatrix, has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.
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Affiliation(s)
- Ana Sofia B Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Diogo Nuno Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Vitor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Dora Batista
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
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9
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Sousa F, Costa J, Ribeiro C, Varandas M, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel C, Veloso MM, Oliveira M, Pinto Ricardo C, Batista D, Paulo OS. Population structure in Quercus suber L. revealed by nuclear microsatellite markers. PeerJ 2022; 10:e13565. [PMID: 35729909 PMCID: PMC9206845 DOI: 10.7717/peerj.13565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure.
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Affiliation(s)
- Filipe Sousa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Joana Costa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,RAIZ, Herdade de Espirra, Pegões, Portugal
| | - Carla Ribeiro
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Marta Varandas
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Francisco Pina-Martins
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Polytechnic Institute of Setúbal, ESTBarreiro, Setúbal, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - José Matos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Maria Glushkova
- Forest Research Institute of B.A.S., Department of Forest Genetics, Physiology and Plantations, Sofia, Bulgaria
| | - Célia Miguel
- Faculdade de Ciências, Universidade de Lisboa, Biosystems & Integrative Sciences Institute, Lisboa, Portugal,iBET, Oeiras, Portugal
| | - Maria Manuela Veloso
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Margarida Oliveira
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cândido Pinto Ricardo
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Dora Batista
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Instituto Superior de Agronomia, Universidade de Lisboa, LEAF—Linking Landscape, Environment, Agriculture and Food (LEAF), Lisboa, Portugal
| | - Octávio S. Paulo
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
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10
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Santangelo JS, Ness RW, Cohan B, Fitzpatrick CR, Innes SG, Koch S, Miles LS, Munim S, Peres-Neto PR, Prashad C, Tong AT, Aguirre WE, Akinwole PO, Alberti M, Álvarez J, Anderson JT, Anderson JJ, Ando Y, Andrew NR, Angeoletto F, Anstett DN, Anstett J, Aoki-Gonçalves F, Arietta AZA, Arroyo MTK, Austen EJ, Baena-Díaz F, Barker CA, Baylis HA, Beliz JM, Benitez-Mora A, Bickford D, Biedebach G, Blackburn GS, Boehm MMA, Bonser SP, Bonte D, Bragger JR, Branquinho C, Brans KI, Bresciano JC, Brom PD, Bucharova A, Burt B, Cahill JF, Campbell KD, Carlen EJ, Carmona D, Castellanos MC, Centenaro G, Chalen I, Chaves JA, Chávez-Pesqueira M, Chen XY, Chilton AM, Chomiak KM, Cisneros-Heredia DF, Cisse IK, Classen AT, Comerford MS, Fradinger CC, Corney H, Crawford AJ, Crawford KM, Dahirel M, David S, De Haan R, Deacon NJ, Dean C, Del-Val E, Deligiannis EK, Denney D, Dettlaff MA, DiLeo MF, Ding YY, Domínguez-López ME, Dominoni DM, Draud SL, Dyson K, Ellers J, Espinosa CI, Essi L, Falahati-Anbaran M, Falcão JCF, Fargo HT, Fellowes MDE, Fitzpatrick RM, Flaherty LE, Flood PJ, Flores MF, Fornoni J, Foster AG, Frost CJ, Fuentes TL, Fulkerson JR, Gagnon E, Garbsch F, Garroway CJ, Gerstein AC, Giasson MM, Girdler EB, Gkelis S, Godsoe W, Golemiec AM, Golemiec M, González-Lagos C, Gorton AJ, Gotanda KM, Granath G, Greiner S, Griffiths JS, Grilo F, Gundel PE, Hamilton B, Hardin JM, He T, Heard SB, Henriques AF, Hernández-Poveda M, Hetherington-Rauth MC, Hill SJ, Hochuli DF, Hodgins KA, Hood GR, Hopkins GR, Hovanes KA, Howard AR, Hubbard SC, Ibarra-Cerdeña CN, Iñiguez-Armijos C, Jara-Arancio P, Jarrett BJM, Jeannot M, Jiménez-Lobato V, Johnson M, Johnson O, Johnson PP, Johnson R, Josephson MP, Jung MC, Just MG, Kahilainen A, Kailing OS, Kariñho-Betancourt E, Karousou R, Kirn LA, Kirschbaum A, Laine AL, LaMontagne JM, Lampei C, Lara C, Larson EL, Lázaro-Lobo A, Le JH, Leandro DS, Lee C, Lei Y, León CA, Lequerica Tamara ME, Levesque DC, Liao WJ, Ljubotina M, Locke H, Lockett MT, Longo TC, Lundholm JT, MacGillavry T, Mackin CR, Mahmoud AR, Manju IA, Mariën J, Martínez DN, Martínez-Bartolomé M, Meineke EK, Mendoza-Arroyo W, Merritt TJS, Merritt LEL, Migiani G, Minor ES, Mitchell N, Mohammadi Bazargani M, Moles AT, Monk JD, Moore CM, Morales-Morales PA, Moyers BT, Muñoz-Rojas M, Munshi-South J, Murphy SM, Murúa MM, Neila M, Nikolaidis O, Njunjić I, Nosko P, Núñez-Farfán J, Ohgushi T, Olsen KM, Opedal ØH, Ornelas C, Parachnowitsch AL, Paratore AS, Parody-Merino AM, Paule J, Paulo OS, Pena JC, Pfeiffer VW, Pinho P, Piot A, Porth IM, Poulos N, Puentes A, Qu J, Quintero-Vallejo E, Raciti SM, Raeymaekers JAM, Raveala KM, Rennison DJ, Ribeiro MC, Richardson JL, Rivas-Torres G, Rivera BJ, Roddy AB, Rodriguez-Muñoz E, Román JR, Rossi LS, Rowntree JK, Ryan TJ, Salinas S, Sanders NJ, Santiago-Rosario LY, Savage AM, Scheepens JF, Schilthuizen M, Schneider AC, Scholier T, Scott JL, Shaheed SA, Shefferson RP, Shepard CA, Shykoff JA, Silveira G, Smith AD, Solis-Gabriel L, Soro A, Spellman KV, Whitney KS, Starke-Ottich I, Stephan JG, Stephens JD, Szulc J, Szulkin M, Tack AJM, Tamburrino Í, Tate TD, Tergemina E, Theodorou P, Thompson KA, Threlfall CG, Tinghitella RM, Toledo-Chelala L, Tong X, Uroy L, Utsumi S, Vandegehuchte ML, VanWallendael A, Vidal PM, Wadgymar SM, Wang AY, Wang N, Warbrick ML, Whitney KD, Wiesmeier M, Wiles JT, Wu J, Xirocostas ZA, Yan Z, Yao J, Yoder JB, Yoshida O, Zhang J, Zhao Z, Ziter CD, Zuellig MP, Zufall RA, Zurita JE, Zytynska SE, Johnson MTJ. Global urban environmental change drives adaptation in white clover. Science 2022; 375:1275-1281. [PMID: 35298255 DOI: 10.1126/science.abk0989] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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Affiliation(s)
- James S Santangelo
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Beata Cohan
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Simon G Innes
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Biology, University of Louisiana, Lafayette, LA, USA
| | - Sophie Koch
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Lindsay S Miles
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Samreen Munim
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Cindy Prashad
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Alex T Tong
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL, USA
| | | | - Marina Alberti
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Jackie Álvarez
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Joseph J Anderson
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yoshino Ando
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Nigel R Andrew
- Natural History Museum, Zoology, University of New England, Armidale, NSW, Australia
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Geografia da UFMT, campus de Rondonópolis, Cuiabá, Brazil
| | - Daniel N Anstett
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Mary T K Arroyo
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Emily J Austen
- Department of Biology, Mount Allison University, Sackville, NB, Canada
| | | | - Cory A Barker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Howard A Baylis
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Julia M Beliz
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.,Department of Biology, University of Miami, Miami, FL, USA
| | - Alfonso Benitez-Mora
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | - David Bickford
- Department of Biology, University of La Verne, La Verne, CA, USA
| | | | - Gwylim S Blackburn
- Département des sciences du bois et de la forêt, Université Laval, Quebec, QC, Canada
| | - Mannfred M A Boehm
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Stephen P Bonser
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Dries Bonte
- Department of Biology, Ghent University, Ghent, Belgium
| | - Jesse R Bragger
- Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | | | - Jorge C Bresciano
- School of Agriculture and Environment, Wildlife and Ecology group, Massey University, Palmerston North, Manawatu, New Zealand
| | - Peta D Brom
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna Bucharova
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Briana Burt
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Elizabeth J Carlen
- Louis Calder Center and Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - Diego Carmona
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - Giada Centenaro
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Izan Chalen
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,iBIOTROP Instituto de Biodiversidad Tropical, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jaime A Chaves
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Mariana Chávez-Pesqueira
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán AC, Mérida, Yucatán, México
| | - Xiao-Yong Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai 200231, China
| | - Angela M Chilton
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Kristina M Chomiak
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Diego F Cisneros-Heredia
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,iBIOTROP Instituto de Biodiversidad Tropical, Universidad San Francisco de Quito, Quito, Ecuador
| | - Ibrahim K Cisse
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Aimée T Classen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Hannah Corney
- Biology Department, Saint Mary's University, Halifax, NS, Canada
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Kerri M Crawford
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Maxime Dahirel
- ECOBIO (Ecosystèmes, biodiversité, évolution), Université de Rennes, Rennes, France
| | - Santiago David
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Robert De Haan
- Department of Environmental Studies, Dordt University, Sioux Center, IA, USA
| | - Nicholas J Deacon
- Department of Biology, Minneapolis Community and Technical College, Minneapolis, MN, USA
| | - Clare Dean
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK
| | - Ek Del-Val
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Morelia, Mexico
| | | | - Derek Denney
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Michelle F DiLeo
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Yuan-Yuan Ding
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Moisés E Domínguez-López
- Corporación Científica Ingeobosque, Medellín, Antioquia, Colombia.,GTA Colombia S.A.S. Envigado, Antioquia, Colombia
| | - Davide M Dominoni
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | | | - Karen Dyson
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Jacintha Ellers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Carlos I Espinosa
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Liliana Essi
- Departamento de Biologia, Universidade Federal de Santa Maria (UFSM), Santa Maria, Rio Grande do Sul, Brazil
| | - Mohsen Falahati-Anbaran
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran.,NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Jéssica C F Falcão
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, Mexico
| | - Hayden T Fargo
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Mark D E Fellowes
- School of Biological Sciences, University of Reading, Whiteknights Park, Reading, Berkshire, UK
| | | | - Leah E Flaherty
- Department of Biological Sciences, MacEwan University, Edmonton, AB, Canada
| | - Pádraic J Flood
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - María F Flores
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Juan Fornoni
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Amy G Foster
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Tracy L Fuentes
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Justin R Fulkerson
- Alaska Center for Conservation Science, University of Alaska Anchorage, Anchorage, AK, USA
| | - Edeline Gagnon
- Tropical Diversity, Royal Botanical Garden of Edinburgh, Edinburgh, UK.,Département de biologie, Université de Moncton, Moncton, New Brunswick, Canada
| | - Frauke Garbsch
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Aleeza C Gerstein
- Departments of Microbiology & Statistics, University of Manitoba, Winnipeg, MB, Canada
| | - Mischa M Giasson
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | | | - Spyros Gkelis
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - William Godsoe
- BioProtection Research Centre, Lincoln University, Lincoln, Canterbury, New Zealand
| | | | - Mireille Golemiec
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - César González-Lagos
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile.,Departamento de Ciencias, Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Amanda J Gorton
- Department of Ecology, Evolution, and Behaviour University of Minnesota, Minneapolis, MN, USA
| | - Kiyoko M Gotanda
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Gustaf Granath
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Stephan Greiner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joanna S Griffiths
- Department of Environmental Toxicology, University of California, Davis, CA, USA
| | - Filipa Grilo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Pedro E Gundel
- IFEVA, Universidad de Buenos Aires, CONICET, Facultad de Agronomía, Buenos Aires, Argentina.,ICB - University of Talca, Chile
| | - Benjamin Hamilton
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | | | - Tianhua He
- School of Molecular and Life Science, Curtin University, Perth, Australia.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Stephen B Heard
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - André F Henriques
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | | | | | - Sarah J Hill
- Natural History Museum, Zoology, University of New England, Armidale, NSW, Australia
| | - Dieter F Hochuli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Glen R Hood
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Gareth R Hopkins
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | - Katherine A Hovanes
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA
| | - Ava R Howard
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | | | | | - Carlos Iñiguez-Armijos
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Paola Jara-Arancio
- Departamento de Ciencias Biológicas y Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Institute of Ecology and Biodiversity (IEB), Chile
| | - Benjamin J M Jarrett
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Manon Jeannot
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vania Jiménez-Lobato
- Escuela Superiro de Desarrollo Sustentable, Universidad Autónoma de Guerrero -CONACYT, Las Tunas, Mexico
| | - Mae Johnson
- Clarkson Secondary School, Peel District School Board, Mississauga, ON, Canada
| | - Oscar Johnson
- Homelands Sr. Public School, Peel District School Board, Mississauga, ON, Canada
| | - Philip P Johnson
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Reagan Johnson
- St. James Catholic Global Learning Centre, Dufferin-Peel Catholic District School Board, Mississauga ON, Canada
| | | | - Meen Chel Jung
- Department of Urban Design and Planning, University of Washington, Seattle, WA, USA
| | - Michael G Just
- Ecological Processes Branch, U.S. Army ERDC-CERL, Champaign, IL, USA
| | - Aapo Kahilainen
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Otto S Kailing
- Department of Biology, Oberlin College, Oberlin, OH, USA
| | | | - Regina Karousou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lauren A Kirn
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Anna Kirschbaum
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Anna-Liisa Laine
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Jalene M LaMontagne
- Department of Biological Sciences, DePaul University, Chicago, IL, USA.,Urban Wildlife Institute, Department of Conservation and Science, Lincoln Park Zoo, Chicago, IL, USA
| | - Christian Lampei
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Carlos Lara
- Departamento de Ecología, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Adrián Lázaro-Lobo
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
| | - Jennifer H Le
- Department of Biology, Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Deleon S Leandro
- Programa de Pós-Graduação em Geografia da UFMT, campus de Rondonópolis, Brasil
| | - Christopher Lee
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Yunting Lei
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Carolina A León
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | | | - Danica C Levesque
- Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Wan-Jin Liao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Megan Ljubotina
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hannah Locke
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Martin T Lockett
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Tiffany C Longo
- Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | | | - Thomas MacGillavry
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | | | - Alex R Mahmoud
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Isaac A Manju
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | - Janine Mariën
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - D Nayeli Martínez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Morelia, Mexico.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, 04510, Mexico
| | - Marina Martínez-Bartolomé
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA.,Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | | | - Thomas J S Merritt
- Department of Chemistry & Biochemistry, Laurentian University, Sudbury, ON, Canada
| | | | - Giuditta Migiani
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
| | - Emily S Minor
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Nora Mitchell
- Department of Biology, University of New Mexico, Albuquerque, NM, USA.,Department of Biology, University of Wisconsin - Eau Claire, Eau Claire, WI 54701
| | - Mitra Mohammadi Bazargani
- Agriculture Institute, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Angela T Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Julia D Monk
- School of the Environment, Yale University, New Haven, CT, USA
| | | | | | - Brook T Moyers
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Miriam Muñoz-Rojas
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia.,Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Av. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Jason Munshi-South
- Louis Calder Center and Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - Shannon M Murphy
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Maureen M Murúa
- Facultad de Estudios Interdisciplinarios, Centro GEMA- Genómica, Ecología y Medio Ambiente, Universidad Mayor, Santiago, Chile
| | - Melisa Neila
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Santiago, Chile
| | - Ourania Nikolaidis
- Department of Biology, Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Iva Njunjić
- Evolutionary Ecology Group, Naturalis Biodiversity Center, Leiden, Netherlands
| | - Peter Nosko
- Department of Biology and Chemistry, Nipissing University, North Bay, ON, Canada
| | - Juan Núñez-Farfán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Takayuki Ohgushi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Cristina Ornelas
- Bonanza Creek Long Term Ecological Research Program, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Amy L Parachnowitsch
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Aaron S Paratore
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Angela M Parody-Merino
- School of Agriculture and Environment, Wildlife and Ecology group, Massey University, Palmerston North, Manawatu, New Zealand
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - João Carlos Pena
- Departamento de Biodiversidade, Instituto de Biociências, Univ Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | - Vera W Pfeiffer
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, WI, USA
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Anthony Piot
- Département des sciences du bois et de la forêt, Université Laval, Quebec, QC, Canada
| | - Ilga M Porth
- Département des sciences du bois et de la forêt, Université Laval, Quebec, QC, Canada
| | - Nicholas Poulos
- Department of Biology, California State University, Northridge, Los Angeles, CA, USA
| | - Adriana Puentes
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jiao Qu
- Department of Biology, Ghent University, Ghent, Belgium
| | | | - Steve M Raciti
- Department of Biology, Hofstra University, Long Island, NY, USA
| | | | - Krista M Raveala
- Faculty of Biological and Environmental Science, Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Diana J Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
| | - Milton C Ribeiro
- Departamento de Biodiversidade, Instituto de Biociências, Univ Estadual Paulista - UNESP, Rio Claro, São Paulo, Brazil
| | | | - Gonzalo Rivas-Torres
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | | | - Adam B Roddy
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, FL, USA
| | | | | | - Laura S Rossi
- Department of Biology and Chemistry, Nipissing University, North Bay, ON, Canada
| | - Jennifer K Rowntree
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK
| | - Travis J Ryan
- Department of Biological Sciences and Center for Urban Ecology and Sustainability, Butler University, Indianapolis, IN, USA
| | | | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Amy M Savage
- Department of Biology, Center for Computational & Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - J F Scheepens
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Adam C Schneider
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Biology, Hendrix College, Conway, AR, USA
| | - Tiffany Scholier
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jared L Scott
- Department of Biology, University of Louisville, Louisville, KY, USA
| | - Summer A Shaheed
- Department of Biology, Monmouth University, West Long Branch, NJ, USA
| | - Richard P Shefferson
- Organization for Programs on Environmental Science, University of Tokyo, Tokyo, Japan
| | | | - Jacqui A Shykoff
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91405, Orsay, France
| | | | - Alexis D Smith
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Lizet Solis-Gabriel
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, UNAM, Morelia, Mexico
| | - Antonella Soro
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Katie V Spellman
- Bonanza Creek Long Term Ecological Research Program, University of Alaska Fairbanks, Fairbanks, AK, USA.,International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kaitlin Stack Whitney
- Science, Technology and Society Department, Rochester Institute of Technology, Rochester, NY, USA
| | - Indra Starke-Ottich
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Jörg G Stephan
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,SLU Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Justyna Szulc
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Marta Szulkin
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Ítalo Tamburrino
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Tayler D Tate
- Department of Biology, Western Oregon University, Monmouth, OR, USA
| | | | - Panagiotis Theodorou
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ken A Thompson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Caragh G Threlfall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | | | | | - Xin Tong
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Léa Uroy
- ECOBIO (Ecosystèmes, biodiversité, évolution), Université de Rennes, Rennes, France.,UMR 0980 BAGAP, Agrocampus Ouest-ESA-INRA, Rennes, France
| | - Shunsuke Utsumi
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Martijn L Vandegehuchte
- Department of Biology, Ghent University, Ghent, Belgium.,Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Acer VanWallendael
- Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Paula M Vidal
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | | | - Ai-Ying Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China, Hubei, China
| | - Montana L Warbrick
- Department of Biology and Chemistry, Nipissing University, North Bay, ON, Canada
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Miriam Wiesmeier
- School of Life Sciences, Technical University of Munich, Munich, Germany
| | | | - Jianqiang Wu
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zoe A Xirocostas
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China, Hubei, China
| | - Jiahe Yao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jeremy B Yoder
- Department of Biology, California State University, Northridge, Los Angeles, CA, USA
| | - Owen Yoshida
- Biology Department, Saint Mary's University, Halifax, NS, Canada
| | - Jingxiong Zhang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhigang Zhao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Carly D Ziter
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Matthew P Zuellig
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Juan E Zurita
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sharon E Zytynska
- School of Life Sciences, Technical University of Munich, Munich, Germany.,Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Centre for Urban Environments, University of Toronto Mississauga, Mississauga, ON, Canada
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11
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Seabra SG, Rodrigues AS, Silva SE, Neto AC, Pina-Martins F, Marabuto E, Thompson V, Wilson MR, Yurtsever S, Halkka A, Rebelo MT, Borges PA, Quartau JA, Jiggins CD, Paulo OS. Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data. PeerJ 2021; 9:e11425. [PMID: 34131518 PMCID: PMC8176912 DOI: 10.7717/peerj.11425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/17/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.
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Affiliation(s)
- Sofia G. Seabra
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S.B. Rodrigues
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sara E. Silva
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carina Neto
- CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Eduardo Marabuto
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Michael R. Wilson
- National Museum of Wales, Department of Natural Sciences, Cardiff, United Kingdom
| | - Selçuk Yurtsever
- Trakya University, Biology Department, Science Faculty, Edirne, Turkey
| | - Antti Halkka
- Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Maria Teresa Rebelo
- CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Paulo A.V. Borges
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, Faculty of Agriculture and Environment, Department of Environmental Sciences and Engineering, Universidade dos Açores, Angra do Heroísmo, Açores, Portugal
| | - José A. Quartau
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Octávio S. Paulo
- E3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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12
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Vanhove M, Pina‐Martins F, Coelho AC, Branquinho C, Costa A, Batista D, Príncipe A, Sousa P, Henriques A, Marques I, Belkadi B, Knowles LL, Paulo OS. Using gradient Forest to predict climate response and adaptation in Cork oak. J Evol Biol 2021; 34:910-923. [DOI: 10.1111/jeb.13765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Mathieu Vanhove
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Francisco Pina‐Martins
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Ana Cristina Coelho
- Centro de Electrónica, Optoelectronica e Telecomunicações Universidade do Algarve Faro Portugal
| | - Cristina Branquinho
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária Oeiras Portugal
- CENSE ‐ Center for Environmental and Sustainability Research NOVA University of Lisbon Caparica Portugal
| | - Dora Batista
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | - Adriana Príncipe
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Paulo Sousa
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - André Henriques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Isabel Marques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Forest Research Centre Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | | | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Octávio S. Paulo
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
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13
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Ascensão F, D'Amico M, Martins RC, Rebelo R, Barbosa AM, Bencatel J, Barrientos R, Abellán P, Tella JL, Cardador L, Anadón JD, Carrete M, Murgui E, Fernandes P, Santos SM, Mira A, da Luz Mathias M, Tiago P, Casabella E, Reino L, Paulo OS, Pereira HM, Capinha C. Distribution of alien tetrapods in the Iberian Peninsula. NB 2021. [DOI: 10.3897/neobiota.64.55597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present a dataset that assembles occurrence records of alien tetrapods (amphibians, reptiles, birds and mammals) in the Iberian Peninsula, a coherent biogeographically unit where introductions of alien species have occurred for millennia. These data have important potential applications for ecological research and management, including the assessment of invasion risks, formulation of preventive and management plans, and research at the biological community level on alien species. This dataset summarizes inventories and data sources on the taxonomy and distribution of alien tetrapods in the Iberia Peninsula, comprising known locations from published literature, expert knowledge and citizen science platforms. An expert-based assessment process allowed the identification of unreliable records (misclassification or natural dispersion from native range), and the classification of species according to their status of reproduction in the wild. Distributional data was harmonized into a common area unit, the 10 × 10 km Universal Transverse Mercator (UTM) system (n = 6,152 cells). The year of observation and/or year of publication were also assigned to the records. In total, we assembled 35,940 unique distribution records (UTM × species × Year) for 253 species (6 amphibians, 16 reptiles, 218 birds and 13 mammals), spanning between 1912 and 2020. The species with highest number of distribution records were the Mediterranean painted frog Discoglossus pictus (n = 59 UTM), the pond slider Trachemys scripta (n = 471), the common waxbill Estrilda astrild (n = 1,275) and the house mouse Mus musculus (n = 4,043), for amphibians, reptiles, birds and mammals, respectively. Most alien species recorded are native to Africa (33%), followed by South America (21%), Asia (19%), North America (12%) and Oceania (10%). Thirty-six species are classified by IUCN as threatened in their native range, namely 2 Critically Endangered (CR), 6 Endangered (EN), 8 Vulnerable (VU), and 20 species Near Threatened (NT). Species maps are provided in DataSet1, as well R code and GIS layers to update them as new records are obtained.
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14
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Marques I, Fernandes I, David PH, Paulo OS, Goulao LF, Fortunato AS, Lidon FC, DaMatta FM, Ramalho JC, Ribeiro-Barros AI. Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO 2]. Int J Mol Sci 2020; 21:ijms21239211. [PMID: 33287164 PMCID: PMC7730880 DOI: 10.3390/ijms21239211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023] Open
Abstract
As atmospheric [CO2] continues to rise to unprecedented levels, understanding its impact on plants is imperative to improve crop performance and sustainability under future climate conditions. In this context, transcriptional changes promoted by elevated CO2 (eCO2) were studied in genotypes from the two major traded coffee species: the allopolyploid Coffea arabica (Icatu) and its diploid parent, C. canephora (CL153). While Icatu expressed more genes than CL153, a higher number of differentially expressed genes were found in CL153 as a response to eCO2. Although many genes were found to be commonly expressed by the two genotypes under eCO2, unique genes and pathways differed between them, with CL153 showing more enriched GO terms and metabolic pathways than Icatu. Divergent functional categories and significantly enriched pathways were found in these genotypes, which altogether supports contrasting responses to eCO2. A considerable number of genes linked to coffee physiological and biochemical responses were found to be affected by eCO2 with the significant upregulation of photosynthetic, antioxidant, and lipidic genes. This supports the absence of photosynthesis down-regulation and, therefore, the maintenance of increased photosynthetic potential promoted by eCO2 in these coffee genotypes.
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Affiliation(s)
- Isabel Marques
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 2784-505 Oeiras and Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (P.H.D.); (O.S.P.)
- Correspondence: (I.M.); (J.C.R.); (A.I.R.-B.)
| | - Isabel Fernandes
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (P.H.D.); (O.S.P.)
| | - Pedro H.C. David
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (P.H.D.); (O.S.P.)
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.F.); (P.H.D.); (O.S.P.)
| | - Luis F. Goulao
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal;
| | - Ana S. Fortunato
- GREEN-IT—Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade NOVA de Lisboa (UNL), Av. da República, 2780-157 Oeiras, Portugal;
| | - Fernando C. Lidon
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal;
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa 36570-900 (MG), Brazil;
| | - José C. Ramalho
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 2784-505 Oeiras and Tapada da Ajuda, 1349-017 Lisboa, Portugal
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal;
- Correspondence: (I.M.); (J.C.R.); (A.I.R.-B.)
| | - Ana I. Ribeiro-Barros
- Plant-Environment Interactions and Biodiversity Lab (PlantStress & Biodiversity), Forest Research Centre (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 2784-505 Oeiras and Tapada da Ajuda, 1349-017 Lisboa, Portugal
- GeoBioSciences, GeoTechnologies and GeoEngineering (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Monte de Caparica, Portugal;
- Correspondence: (I.M.); (J.C.R.); (A.I.R.-B.)
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15
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Marabuto E, Pina-Martins F, Rebelo MT, Paulo OS. Ancient divergence, a crisis of salt and another of ice shaped the evolution of the west Mediterranean butterfly Euchloe tagis. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractThe Mediterranean region is an extremely complex hotspot where, since the Miocene, extensive geological, habitat and climate changes have taken place, alternating between warm and cold periods. These phenomena have taken a toll on the genetic composition of species, and surviving lineages have often adapted locally and diverged to the point of (complete) speciation. To study these phenomena, in this study we used one of the most enigmatic butterflies, the Portuguese dappled white, Euchloe tagis, a west Mediterranean endemic with fragmented, morphologically differentiated populations whose status have long been disputed. Even its affiliations with other Anthocharidini are largely unresolved. We used mitochondrial and nuclear markers under a phylogenetic and phylogeographical framework to evaluate its placement among relatives and population differentiation, reconstructing its evolutionary history. We found that this species had a Miocene origin ~15 Mya and was nearest to Euchloe s.s. and Elphinstonia. Its populations showed high genetic diversity but all coalesced to 5.3 Mya, when European and all but one African population diverged. Our multiple findings concerning the evolution of E. tagis through a changing, narrow habitable area might provide a more general perspective on how species survive within this hotspot of paramount importance.
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Affiliation(s)
- Eduardo Marabuto
- Computational Biology and Population Genomics Group, cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Maria Teresa Rebelo
- Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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16
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Seabra SG, Pina-Martins F, Marabuto E, Yurtsever S, Halkka O, Quartau JA, Paulo OS. Corrigendum to "Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species" [Mol. Phylogenet. Evol. 56 (2010) 462-467]. Mol Phylogenet Evol 2020; 152:106888. [PMID: 32781419 DOI: 10.1016/j.ympev.2020.106888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- S G Seabra
- Centro de Biologia Ambiental/Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016 Lisboa, Portugal.
| | - F Pina-Martins
- Centro de Biologia Ambiental/Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016 Lisboa, Portugal
| | - E Marabuto
- Centro de Biologia Ambiental/Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016 Lisboa, Portugal
| | - S Yurtsever
- Biology Department, Faculty of the Arts and Science, Trakya University, 22030 Edirne, Turkey
| | - O Halkka
- Tvärminne Zoological Station, University of Helsinki, Finland
| | - J A Quartau
- Centro de Biologia Ambiental/Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016 Lisboa, Portugal
| | - O S Paulo
- Centro de Biologia Ambiental/Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016 Lisboa, Portugal
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17
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Rodrigues ASB, Silva SE, Pina-Martins F, Loureiro J, Castro M, Gharbi K, Johnson KP, Dietrich CH, Borges PAV, Quartau JA, Jiggins CD, Paulo OS, Seabra SG. Correction to: Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources. BMC Genet 2020; 21:36. [PMID: 32209049 PMCID: PMC7092421 DOI: 10.1186/s12863-020-00842-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ana S B Rodrigues
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal.
| | - Sara E Silva
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal.,Centro de Estudos do Ambiente e do Mar (CESAM), DBA/FCUL, Lisbon, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Mariana Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Paulo A V Borges
- Departamento de Ciências e Engenharia do Ambiente, Angra do Heroísmo, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Açores, Portugal
| | - José A Quartau
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal
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18
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Neves A, Vieira AR, Sequeira V, Paiva RB, Gordo LS, Paulo OS. Highly regional population structure of Spondyliosoma cantharus depicted by nuclear and mitochondrial DNA data. Sci Rep 2020; 10:4063. [PMID: 32132605 PMCID: PMC7055218 DOI: 10.1038/s41598-020-61050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/20/2020] [Indexed: 12/24/2022] Open
Abstract
Resolution of population structure represents an effective way to define biological stocks and inform efficient fisheries management. In the present study, the phylogeography of the protogynous sparid Spondyliosoma cantharus, in the East Atlantic and Mediterranean Sea, was investigated with nuclear (S7) and mitochondrial (cytochrome b) DNA markers. Significant divergence of four regional genetic groups was observed: North Eastern Atlantic, Mediterranean Sea, Western African Transition (Cape Verde) and Gulf of Guinea (Angola). The two southern populations (Cape Verde and Angola) each comprised reciprocally monophyletic mtDNA lineages, revealed low levels of diversity in Cape Verde and high diversity for Angola despite being represented by only 14 individuals. A complete divergence between North Atlantic and Mediterranean populations was depicted by the mitochondrial marker, but a highly shared nuclear haplotype revealed an incomplete lineage sorting between these regions. Bayesian skyline plots and associated statistics revealed different dynamics among the four regions. Cape Verde showed no expansion and the expansion time estimated for Angola was much older than for the other regions. Mediterranean region seems to have experienced an early population growth but has remained with a stable population size for the last 30000 years while the North Atlantic population has been steadily growing. The lack of genetic structuring within these regions should not be taken as evidence of demographic panmixia in light of potential resolution thresholds and previous evidence of intra-regional phenotypic heterogeneity.
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Affiliation(s)
- Ana Neves
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal. .,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Ana Rita Vieira
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Vera Sequeira
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Rafaela Barros Paiva
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Leonel Serrano Gordo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Octávio S Paulo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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19
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Malumbres-Olarte J, Boieiro M, Cardoso P, Carvalho R, Crespo LCF, Gabriel R, Macías Hernández N, Paulo OS, Pereira F, Rego C, Ros-Prieto A, Silva I, Vieira A, Rigal F, Borges PAV. Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia II: The native forests and dry habitats of Madeira archipelago (Madeira and Porto Santo islands). Biodivers Data J 2020; 8:e47502. [PMID: 31992947 PMCID: PMC6974486 DOI: 10.3897/bdj.8.e47502] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/12/2019] [Indexed: 12/30/2022] Open
Abstract
Background Here we present the data obtained from the samples collected as part of a large research project (MACDIV) which aims at understanding the drivers of spider (Araneae) community assembly in Macaronesian islands. To obtain the data, we applied the sampling protocol COBRA (Conservation Oriented Biodiversity Rapid Assessment), in twelve 50 m x 50 m native forest plots and five dry habitat plots on the island of Madeiraand in 5 dry habitat plots on the island of Porto Santo. Through this publication, we contribute to the knowledge of the arachnofauna of the Madeiran archipelago. New information From the samples that we collected, we obtained a total of 14,902 specimens, of which 49% were adults (7,263). We identified these specimens to 87 species and 18 morphospecies (undescribed), belonging to 26 families. Species of the family Linyphiidae dominated the samples, with 24 (morpho)species. Out of the 105 recorded (morpho)species, 34 were endemic, 26 native non-endemic, 22 introduced and 23 species of unknown origin. We report seven new records of possibly recently introduced species in the Madeiran archipelago. We also present 21 new records for Madeira island and 32 for Porto Santo (33 for the whole archipelago).
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Affiliation(s)
- Jagoba Malumbres-Olarte
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal.,LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki Helsinki Finland
| | - Mário Boieiro
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Pedro Cardoso
- LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki Helsinki Finland.,IUCN SSC Spider & Scorpion Specialist Group, Helsinki, Finland IUCN SSC Spider & Scorpion Specialist Group Helsinki Finland.,CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Rui Carvalho
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Luís Carlos Fonseca Crespo
- Biodiversity Research Institute UB, Departament Department of Evolutionary Biology, Ecology and Environmental Sciences (Arthropods), Barcelona, Spain Biodiversity Research Institute UB, Departament Department of Evolutionary Biology, Ecology and Environmental Sciences (Arthropods) Barcelona Spain.,LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki Helsinki Finland
| | - Rosalina Gabriel
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Nuria Macías Hernández
- LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland LIBRe - Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki Helsinki Finland.,Island Ecology and Evolution Research Group, IPNA-CSIC, Tenerife, Canary Islands, Spain Island Ecology and Evolution Research Group, IPNA-CSIC Tenerife, Canary Islands Spain
| | - Octávio S Paulo
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Lisbon, Portugal Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group Lisbon Portugal
| | - Fernando Pereira
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Carla Rego
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Alejandra Ros-Prieto
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Isamberto Silva
- Instituto das Florestas e da Conservação da Natureza, Funchal, Portugal Instituto das Florestas e da Conservação da Natureza Funchal Portugal
| | - Ana Vieira
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Lisbon, Portugal Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group Lisbon Portugal
| | - François Rigal
- Environment and Microbiology Team, Université de Pau et des Pays de l'Adour, Pau Cedex, France Environment and Microbiology Team, Université de Pau et des Pays de l'Adour Pau Cedex France.,CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal
| | - Paulo A V Borges
- CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores Angra do Heroísmo, Azores Portugal.,IUCN - SSC Mid-Atlantic Island Invertebrates Specialist Group, Angra do Heroísmo, Azores, Portugal IUCN - SSC Mid-Atlantic Island Invertebrates Specialist Group Angra do Heroísmo, Azores Portugal
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20
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Silva SE, Seabra SG, Carvalheiro LG, Nunes VL, Marabuto E, Mendes R, Rodrigues ASB, Pina-Martins F, Yurtsever S, Laurentino TG, Figueiredo E, Rebelo MT, Paulo OS. Population genomics of Bombus terrestris reveals high but unstructured genetic diversity in a potential glacial refugium. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Ongoing climate change is expected to cause an increase in temperature and a reduction of precipitation levels in the Mediterranean region, which might cause changes in many species distributions. These effects negatively influence species gene pools, decreasing genetic variability and adaptive potential. Here, we use mitochondrial DNA and RADseq to analyse population genetic structure and genetic diversity of the bumblebee species Bombus terrestris (subspecies Bombus terrestris lusitanicus), in the Iberian Peninsula. Although this subspecies shows a panmictic pattern of population structure across Iberia and beyond, we found differentiation between subspecies B. t. lusitanicus and B. t. africanus, probably caused by the existence of barriers to gene flow between Iberia and North Africa. Furthermore, the results revealed that the Iberian Peninsula harbours a large fraction of B. terrestris intraspecific genetic variation, with the highest number of mitochondrial haplotypes found when compared with any other region in Europe studied so far, suggesting a potential role for the Iberian Peninsula as a glacial refugium. Our findings strengthen the idea that Iberia is a very important source of diversity for the global genetic pool of this species, because rare alleles might play a role in population resilience against human- or climate-mediated changes.
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Affiliation(s)
- Sara E Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sofia G Seabra
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luísa G Carvalheiro
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Department of Ecology, Universidade Federal de Goiás, Goiânia, Brazil
| | - Vera L Nunes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Raquel Mendes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S B Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Selçuk Yurtsever
- Biology Department, Science Faculty, Trakya University, Edirne, Turkey
| | | | - Elisabete Figueiredo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - Maria T Rebelo
- Centre for Environmental and Marine Research (CESAM), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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21
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Romeiras MM, Pena AR, Menezes T, Vasconcelos R, Monteiro F, Paulo OS, Moura M. Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity. Int J Mol Sci 2019; 20:E2782. [PMID: 31174340 PMCID: PMC6600550 DOI: 10.3390/ijms20112782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/16/2019] [Accepted: 06/04/2019] [Indexed: 12/22/2022] Open
Abstract
Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.
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Affiliation(s)
- Maria M Romeiras
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Ana Rita Pena
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Tiago Menezes
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
| | - Raquel Vasconcelos
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Filipa Monteiro
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Mónica Moura
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
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22
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Seabra SG, Silva SE, Nunes VL, Sousa VC, Martins J, Marabuto E, Rodrigues ASB, Pina‐Martins F, Laurentino TG, Rebelo MT, Figueiredo E, Paulo OS. Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in western Iberian Peninsula-Implications for conservation and trade regulation. Evol Appl 2019; 12:679-691. [PMID: 30976302 PMCID: PMC6439495 DOI: 10.1111/eva.12732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/24/2018] [Accepted: 10/27/2018] [Indexed: 01/02/2023] Open
Abstract
Human-mediated introductions of species may have profound impacts on native ecosystems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pollination with known negative impacts on native pollinators. Given the likely allochthonous origin of commercial bumblebees used in Portugal (subspecies Bombus terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgression with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mitochondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome-wide restriction-site-associated DNA markers (RAD-seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the greenhouses where the commercial hives are used. In the RAD-seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore, we detected candidate hybrids in the wild, as well as putatively escaped commercial bumblebees, some of which being potentially fertile males. Although we cannot assess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibility of using local subspecies B. t. lusitanicus, preferably with local production, should be evaluated.
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Affiliation(s)
- Sofia G. Seabra
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Sara E. Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Vera L. Nunes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Vitor C. Sousa
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Joana Martins
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
- Present address:
SAPEC AgroLisboaPortugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Ana S. B. Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Natural History and Systematics (NHS) Research Group /MUHNAC ‐ Museu Nacional de História Natural e da CiênciaUniversidade de LisboaLisboaPortugal
| | - Francisco Pina‐Martins
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | - Maria Teresa Rebelo
- Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Elisabete Figueiredo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
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Pina-Martins F, Baptista J, Pappas G, Paulo OS. New insights into adaptation and population structure of cork oak using genotyping by sequencing. Glob Chang Biol 2019; 25:337-350. [PMID: 30358018 DOI: 10.1111/gcb.14497] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 05/25/2023]
Abstract
Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms.
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Affiliation(s)
- Francisco Pina-Martins
- Computational Biology and Population Genomics Group, Departamento de Biologia Animal, Faculdade de Ciências, Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
| | - João Baptista
- Department of Biology, CESAM, University of Aveiro, Aveiro, Portugal
| | - Georgios Pappas
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, Departamento de Biologia Animal, Faculdade de Ciências, Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
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24
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Monteiro F, Frese L, Castro S, Duarte MC, Paulo OS, Loureiro J, Romeiras MM. Genetic and Genomic Tools to Asssist Sugar Beet Improvement: The Value of the Crop Wild Relatives. Front Plant Sci 2018; 9:74. [PMID: 29467772 PMCID: PMC5808244 DOI: 10.3389/fpls.2018.00074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
Sugar beet (Beta vulgaris L. ssp. vulgaris) is one of the most important European crops for both food and sugar production. Crop improvement has been developed to enhance productivity, sugar content or other breeder's desirable traits. The introgression of traits from Crop Wild Relatives (CWR) has been done essentially for lessening biotic stresses constraints, namely using Beta and Patellifolia species which exhibit disease resistance characteristics. Several studies have addressed crop-to-wild gene flow, yet, for breeding programs genetic variability associated with agronomically important traits remains unexplored regarding abiotic factors. To accomplish such association from phenotype-to-genotype, screening for wild relatives occurring in habitats where selective pressures are in play (i.e., populations in salt marshes for salinity tolerance; populations subjected to pathogen attacks and likely evolved resistance to pathogens) are the most appropriate streamline to identify causal genetic information. By selecting sugar beet CWR species based on genomic tools, rather than random variations, is a promising but still seldom explored route toward the development of improved crops. In this perspective, a viable streamline for sugar beet improvement is proposed through the use of different genomic tools by recurring to sugar beet CWRs and focusing on agronomic traits associated with abiotic stress tolerance. Overall, identification of genomic and epigenomic landscapes associated to adaptive ecotypes, along with the cytogenetic and habitat characterization of sugar beet CWR, will enable to identify potential hotspots for agrobiodiversity of sugar beet crop improvement toward abiotic stress tolerance.
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Affiliation(s)
- Filipa Monteiro
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Lothar Frese
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Quedlinburg, Germany
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria C. Duarte
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria M. Romeiras
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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25
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Pina-Martins F, Silva DN, Fino J, Paulo OS. Structure_threader
: An improved method for automation and parallelization of programs structure
, fastStructure
and MavericK
on multicore CPU systems. Mol Ecol Resour 2017; 17:e268-e274. [DOI: 10.1111/1755-0998.12702] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Francisco Pina-Martins
- Computational Biology and Population Genomics Group; Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
- Departamento de Biologia e CESAM; Univ. de Aveiro; Aveiro Portugal
| | - Diogo N. Silva
- Computational Biology and Population Genomics Group; Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
- Instituto Superior de Agronomia; Universidade de Lisboa; CIFC -Centro de Investigação das Ferrugens do Cafeeiro; Oeiras Portugal
| | - Joana Fino
- Computational Biology and Population Genomics Group; Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
- Department of Human Genetics; National Institute of Health Dr Ricardo Jorge; Lisbon Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group; Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; Lisboa Portugal
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26
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Costa GJ, Nunes VL, Marabuto E, Mendes R, Laurentino TG, Quartau JA, Paulo OS, Simões PC. Morphology, songs and genetics identify two new cicada species from Morocco: <i>Tettigettalna</i> <i>afroamissa</i> sp. nov. and <i>Berberigetta</i> <i>dimelodica</i> gen. nov. & sp. nov. (Hemiptera: Cicadettini). Zootaxa 2017; 4237:zootaxa.4237.3.4. [PMID: 28264279 DOI: 10.11646/zootaxa.4237.3.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 11/04/2022]
Abstract
Morocco has been the subject of very few expeditions on the last century with the objective of studying small cicadas. In the summer of 2014 an expedition was carried out to Morocco to update our knowledge with acoustic recordings and genetic data of these poorly known species. We describe here two new small-sized cicadas that could not be directly assigned to any species of North African cicadas: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. In respect to T. afroamissa it is the first species of the genus to be found outside Europe and we frame this taxon within the evolutionary history of the genus. Acoustic analysis of this species allows us to confidently separate T. afroamissa from its congeners. With B. dimelodica, a small species showing a remarkable calling song characterized by an abrupt frequency modulation, a new genus had to be erected. Bayesian inference and maximum likelihood phylogenetic analyses with DNA-barcode sequences of Cytochrome C Oxidase 1 support the monophyly of both species, their distinctness and revealed genetic structure within B. dimelodica. Alongside the descriptions we also provide GPS coordinates of collection points, distributions and habitat preferences.
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Affiliation(s)
- Gonçalo João Costa
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal..
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27
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Ramos MJN, Coito JL, Fino J, Cunha J, Silva H, de Almeida PG, Costa MMR, Amâncio S, Paulo OS, Rocheta M. Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification. Plant Mol Biol 2017; 93:151-170. [PMID: 27778293 DOI: 10.1007/s11103-016-0553-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/15/2016] [Indexed: 06/06/2023]
Abstract
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development.
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Affiliation(s)
- Miguel Jesus Nunes Ramos
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - João Lucas Coito
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - Joana Fino
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d'Almoinha, Dois Portos, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Silva
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Patrícia Gomes de Almeida
- Development and Evolutionary Morphogenesis, Centre for Ecology, Evolution and Environmental Change, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Maria Manuela Ribeiro Costa
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara Amâncio
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Margarida Rocheta
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal.
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28
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Vieira AR, Rodrigues ASB, Sequeira V, Neves A, Paiva RB, Paulo OS, Gordo LS. Genetic and Morphological Variation of the Forkbeard, Phycis phycis (Pisces, Phycidae): Evidence of Panmixia and Recent Population Expansion along Its Distribution Area. PLoS One 2016; 11:e0167045. [PMID: 27941988 PMCID: PMC5152830 DOI: 10.1371/journal.pone.0167045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/11/2016] [Indexed: 12/21/2022] Open
Abstract
The knowledge of population structure of a species is essential to effectively assess and manage fisheries. In the present study, genetics, by mitochondrial DNA cytochrome b sequence analysis, and body geometric morphometrics were used to evaluate the existence of distinct populations of the forkbeard (Phycis phycis), an important commercial species in several European countries, especially Portugal and Spain. For geometric morphometric analysis, specimens were collected in the Northeast Atlantic Ocean—Azores, Madeira and mainland Portugal, and for genetic analysis, these samples were complemented with samples collected in the Mediterranean Sea—Spain, Italy and Croatia, in order to cover the entire distribution area of the species. Body shape of the forkbeard from the Northeast Atlantic was found to be highly variable. This variation was probably associated with different environmental factors between the study areas. Despite morphological variation, a low genetic differentiation between samples from different areas was found, most likely due to gene flow that occurred in the past or with the demographic history of the species. Moreover, the presence of unique haplotypes in the Northeast Atlantic and in the Mediterranean suggests that recent gene flow between populations from these areas should be limited. Altogether, a high haplotype diversity, a low nucleotide diversity, a “star-like” network and the results of the mismatch distribution, indicate a possible signature of recent population expansions, which probably started during the end of the Last Glacial Maximum and led to the colonization of the Northeast Atlantic and the Mediterranean.
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Affiliation(s)
- Ana Rita Vieira
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| | - Ana Sofia B. Rodrigues
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Vera Sequeira
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Neves
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Rafaela Barros Paiva
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Leonel Serrano Gordo
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Figueiredo J, Costa GJ, Maia M, Paulo OS, Malhó R, Sousa Silva M, Figueiredo A. Revisiting Vitis vinifera Subtilase Gene Family: A Possible Role in Grapevine Resistance against Plasmopara viticola. Front Plant Sci 2016; 7:1783. [PMID: 27933087 PMCID: PMC5122586 DOI: 10.3389/fpls.2016.01783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/11/2016] [Indexed: 05/08/2023]
Abstract
Subtilisin-like proteases, also known as subtilases, are a very diverse family of serine peptidases present in many organisms. In grapevine, there are hints of the involvement of subtilases in defense mechanisms, but their role is not yet understood. The first characterization of the subtilase gene family was performed in 2014. However, simultaneously, the grapevine genome was re-annotated and several sequences were re-annotated or retrieved. We have performed a re-characterization of this family in grapevine and identified 82 genes coding for 97 putative proteins, as result of alternative splicing. All the subtilases identified present the characteristic S8 peptidase domain and the majority of them also have a pro-domain I9 inhibitor, a protease-associated (PA) domain, and a signal peptide for targeting to the secretory pathway. Phylogenetic studies revealed six subtilase groups denominated VvSBT1 to VvSBT6. As several evidences have highlighted the participation of plant subtilases in response to biotic stimulus, we have investigated subtilase participation in grapevine resistance to Plasmopara viticola, the causative agent of downy mildew. Fourteen grapevine subtilases presenting either high homology to P69C from tomato, SBT3.3 from Arabidopsis thaliana or located near the Resistance to P. viticola (RPV) locus were selected. Expression studies were conducted in the grapevine-P. viticola pathosystem with resistant and susceptible cultivars. Our results may indicate that some of grapevine subtilisins are potentially participating in the defense response against this biotrophic oomycete.
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Affiliation(s)
- Joana Figueiredo
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Gonçalo J. Costa
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Marisa Maia
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Rui Malhó
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
| | - Andreia Figueiredo
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de LisboaLisboa, Portugal
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Rodrigues ASB, Silva SE, Pina-Martins F, Loureiro J, Castro M, Gharbi K, Johnson KP, Dietrich CH, Borges PAV, Quartau JA, Jiggins CD, Paulo OS, Seabra SG. Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources. BMC Genet 2016; 17:144. [PMID: 27846816 PMCID: PMC5111214 DOI: 10.1186/s12863-016-0455-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 11/07/2016] [Indexed: 01/08/2023] Open
Abstract
Background Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes underlying phenotypic evolution. The meadow spittlebug, Philaenus spumarius (L.) (Hemiptera, Aphrophoridae), a widespread insect species in the Holarctic region, exhibits a striking dorsal colour/pattern balanced polymorphism. Although experimental crosses have revealed the Mendelian inheritance of this trait, its genetic basis remains unknown. In this study we aimed to identify candidate genomic regions associated with the colour balanced polymorphism in this species. Results By using restriction site-associated DNA (RAD) sequencing we were able to obtain a set of 1,837 markers across 33 individuals to test for associations with three dorsal colour phenotypes (typicus, marginellus, and trilineatus). Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour morphs. The genome size of P. spumarius was estimated by flow cytometry, revealing a 5.3 Gb genome, amongst the largest found in insects. A partial genome assembly, representing 24% of the total size, and an 81.4 Mb transcriptome, were also obtained. From the SNPs found to be associated with colour, 35% aligned to the genome and 10% to the transcriptome. Our data suggested that major loci, consisting of multi-genomic regions, may be involved in dorsal colour variation among the three dorsal colour morphs analysed. However, no homology was found between the associated loci and candidate genes known to be responsible for coloration pattern in other insect species. The associated markers showed stronger differentiation of the trilineatus colour phenotype, which has been shown previously to be more differentiated in several life-history and physiological characteristics as well. It is possible that colour variation and these traits are linked in a complex genetic architecture. Conclusions The loci detected to have an association with colour and the genomic and transcriptomic resources developed here constitute a basis for further research on the genetic basis of colour pattern in the meadow spittlebug P. spumarius. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0455-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana S B Rodrigues
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal.
| | - Sara E Silva
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Francisco Pina-Martins
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal.,Centro de Estudos do Ambiente e do Mar (CESAM), DBA/FCUL, Lisbon, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Paulo A V Borges
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências e Engenharia do Ambiente, Angra do Heroísmo, Açores, Portugal
| | - José A Quartau
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
| | - Sofia G Seabra
- Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisbon, P-1749-016, Portugal
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Lopes-Lima M, Froufe E, Do VT, Ghamizi M, Mock KE, Kebapçı Ü, Klishko O, Kovitvadhi S, Kovitvadhi U, Paulo OS, Pfeiffer JM, Raley M, Riccardi N, Şereflişan H, Sousa R, Teixeira A, Varandas S, Wu X, Zanatta DT, Zieritz A, Bogan AE. Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes. Mol Phylogenet Evol 2016; 106:174-191. [PMID: 27621130 DOI: 10.1016/j.ympev.2016.08.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/08/2016] [Accepted: 08/30/2016] [Indexed: 11/15/2022]
Abstract
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.
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Affiliation(s)
- Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Van Tu Do
- Department of Aquatic Ecology, Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Viet Nam
| | - Mohamed Ghamizi
- Muséum d'Histoire Naturelle de Marrakech, Université Cadi Ayyad, Faculté des Sciences, Semlalia, B.P. 2390 Marrakech, Morocco
| | - Karen E Mock
- Ecology Center and Department of Wildland Resources, Utah State University, Logan, UT 84322, USA
| | - Ümit Kebapçı
- Department of Biology, Faculty of Arts and Sciences, Mehmet Akif Ersoy University, Burdur, Turkey
| | - Olga Klishko
- Institute of Natural Resources, Ecology and Criology, Russian Academy of Sciences Siberian Branch, Chita 672014, Russia
| | - Satit Kovitvadhi
- Department of Agriculture, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok 10600, Thailand
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c - Centre for Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - John M Pfeiffer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | | | - Hülya Şereflişan
- Faculty of Marine Sciences and Technology, İskenderun Technical University, 31200 Iskenderun, Hatay, Turkey
| | - Ronaldo Sousa
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - Amílcar Teixeira
- CIMO/ESA/IPB - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança, Campus de Santa Apolónia, Apartado 1172, 5301-854 Bragança, Portugal
| | - Simone Varandas
- CITAB/UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, 5000-801 Vila Real, Portugal
| | - Xiaoping Wu
- School of Life Sciences, Center for Watershed Ecology, Institute of Life Science, Nanchang University, Nanchang 330031, People's Republic of China
| | - David T Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences Bldg. 2408, Mount Pleasant, MI 48859, USA
| | - Alexandra Zieritz
- School of Geography, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Malaysia
| | - Arthur E Bogan
- Research Laboratory, North Carolina State Museum of Natural Sciences, MSC 1626, Raleigh, NC 27699-1626, USA
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Romeiras MM, Vieira A, Silva DN, Moura M, Santos-Guerra A, Batista D, Duarte MC, Paulo OS. Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny. PLoS One 2016; 11:e0152456. [PMID: 27031338 PMCID: PMC4816301 DOI: 10.1371/journal.pone.0152456] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 03/15/2016] [Indexed: 01/29/2023] Open
Abstract
The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR). Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae) and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS) and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL) sequences to: (i) investigate the phylogenetic relationships within the Betoideae subfamily, and (ii) elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus) and provide a detailed inference of relationships within this subfamily, revealing: (i) a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii) the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96-5.33 Mya). Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.
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Affiliation(s)
- Maria M. Romeiras
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- * E-mail:
| | - Ana Vieira
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Diogo N. Silva
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Monica Moura
- Research Network in Biodiversity and Evolutionary Biology, Associate Laboratory (CIBIO/InBIO), Universidade do Porto, Vairão, Portugal
- Universidade dos Açores, Dep. Biologia, Ponta Delgada, Portugal
| | | | - Dora Batista
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Maria Cristina Duarte
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Vieira A, Cabral A, Fino J, Azinheira HG, Loureiro A, Talhinhas P, Pires AS, Varzea V, Moncada P, Oliveira H, Silva MDC, Paulo OS, Batista D. Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae. PLoS One 2016; 11:e0150651. [PMID: 26950697 PMCID: PMC4780792 DOI: 10.1371/journal.pone.0150651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/16/2016] [Indexed: 01/01/2023] Open
Abstract
Colletotrichum kahawae is an emergent fungal pathogen causing severe epidemics of Coffee Berry Disease on Arabica coffee crops in Africa. Currently, the molecular mechanisms underlying the Coffea arabica—C. kahawae interaction are still poorly understood, as well as the differences in pathogen aggressiveness, which makes the development of functional studies for this pathosystem a crucial step. Quantitative real time PCR (qPCR) has been one of the most promising approaches to perform gene expression analyses. However, proper data normalization with suitable reference genes is an absolute requirement. In this study, a set of 8 candidate reference genes were selected based on two different approaches (literature and Illumina RNA-seq datasets) to assess the best normalization factor for qPCR expression analysis of C. kahawae samples. The gene expression stability of candidate reference genes was evaluated for four isolates of C. kahawae bearing different aggressiveness patterns (Ang29, Ang67, Zim12 and Que2), at different stages of fungal development and key time points of the plant-fungus interaction process. Gene expression stability was assessed using the pairwise method incorporated in geNorm and the model-based method used by NormFinder software. For C. arabica—C. kahawae interaction samples, the best normalization factor included the combination of PP1, Act and ck34620 genes, while for C. kahawae samples the combination of PP1, Act and ck20430 revealed to be the most appropriate choice. These results suggest that RNA-seq analyses can provide alternative sources of reference genes in addition to classical reference genes. The analysis of expression profiles of bifunctional catalase-peroxidase (cat2) and trihydroxynaphthalene reductase (thr1) genes further enabled the validation of the selected reference genes. This study provides, for the first time, the tools required to conduct accurate qPCR studies in C. kahawae considering its aggressiveness pattern, developmental stage and host interaction.
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Affiliation(s)
- Ana Vieira
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- Computational Biology and Population Genomics group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Cabral
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| | - Joana Fino
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- Computational Biology and Population Genomics group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Helena G. Azinheira
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Andreia Loureiro
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Talhinhas
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
- Plant Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana Sofia Pires
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- Plant Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vitor Varzea
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | | | - Helena Oliveira
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Maria do Céu Silva
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Dora Batista
- CIFC—Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- Computational Biology and Population Genomics group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- LEAF-Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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Domingos S, Fino J, Paulo OS, Oliveira CM, Goulao LF. Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles. Plant Sci 2016; 244:40-56. [PMID: 26810452 DOI: 10.1016/j.plantsci.2015.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/08/2015] [Accepted: 12/18/2015] [Indexed: 05/23/2023]
Abstract
Flower-to-fruit transition depends of nutrient availability and regulation at the molecular level by sugar and hormone signalling crosstalk. However, in most species, the identities of fruit initiation regulators and their targets are largely unknown. To ascertain the main pathways involved in stenospermocarpic table grape fruit set, comprehensive transcriptional and metabolomic analyses were conducted specifically targeting the early phase of this developmental stage in 'Thompson Seedless'. The high-throughput analyses performed disclosed the involvement of 496 differentially expressed genes and 28 differently accumulated metabolites in the sampled inflorescences. Our data show broad transcriptome reprogramming of molecule transporters, globally down-regulating gene expression, and suggest that regulation of sugar- and hormone-mediated pathways determines the downstream activation of berry development. The most affected gene was the SWEET14 sugar transporter. Hormone-related transcription changes were observed associated with increased indole-3-acetic acid, stimulation of ethylene and gibberellin metabolisms and cytokinin degradation, and regulation of MADS-box and AP2-like ethylene-responsive transcription factor expression. Secondary metabolism, the most representative biological process at transcriptome level, was predominantly repressed. The results add to the knowledge of molecular events occurring in grapevine inflorescence fruit set and provide a list of candidates, paving the way for genetic manipulation aimed at model research and plant breeding.
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Affiliation(s)
- Sara Domingos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Lisbon, Portugal; BioTrop, Instituto de Investigação Científica Tropical I.P. (IICT), Lisbon, Portugal
| | - Joana Fino
- Computational Biology and Population Genomics Group, cE3c-Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, cE3c-Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Cristina M Oliveira
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Lisbon, Portugal
| | - Luis F Goulao
- BioTrop, Instituto de Investigação Científica Tropical I.P. (IICT), Lisbon, Portugal.
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Domingos S, Fino J, Cardoso V, Sánchez C, Ramalho JC, Larcher R, Paulo OS, Oliveira CM, Goulao LF. Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L. BMC Plant Biol 2016; 16:38. [PMID: 26832927 PMCID: PMC4736245 DOI: 10.1186/s12870-016-0722-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/21/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Abscission is a highly coordinated developmental process by which plants control vegetative and reproductive organs load. Aiming at get new insights on flower abscission regulation, changes in the global transcriptome, metabolome and physiology were analyzed in 'Thompson Seedless' grapevine (Vitis vinifera L.) inflorescences, using gibberellic acid (GAc) spraying and shading as abscission stimuli, applied at bloom. RESULTS Natural flower drop rates increased from 63.1% in non-treated vines to 83% and 99% in response to GAc and shade treatments, respectively. Both treatments had a broad effect on inflorescences metabolism. Specific impacts from shade included photosynthesis inhibition, associated nutritional stress, carbon/nitrogen imbalance and cell division repression, whereas GAc spraying induced energetic metabolism simultaneously with induction of nucleotide biosynthesis and carbon metabolism, therefore, disclosing alternative mechanisms to regulate abscission. Regarding secondary metabolism, changes in flavonoid metabolism were the most represented metabolic pathways in the samples collected following GAc treatment while phenylpropanoid and stilbenoid related pathways were predominantly affected in the inflorescences by the shade treatment. However, both GAc and shade treated inflorescences revealed also shared pathways, that involved the regulation of putrescine catabolism, the repression of gibberellin biosynthesis, the induction of auxin biosynthesis and the activation of ethylene signaling pathways and antioxidant mechanisms, although often the quantitative changes occurred on specific transcripts and metabolites of the pathways. CONCLUSIONS Globally, the results suggest that chemical and environmental cues induced contrasting effects on inflorescence metabolism, triggering flower abscission by different mechanisms and pinpointing the participation of novel abscission regulators. Grapevine showed to be considered a valid model to study molecular pathways of flower abscission competence acquisition, noticeably responding to independent stimuli.
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Affiliation(s)
- Sara Domingos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal.
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
| | - Joana Fino
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
| | - Vânia Cardoso
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
| | - Claudia Sánchez
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Oeiras, Portugal.
| | - José C Ramalho
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal.
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
- GeoBioTec, Faculdade de Ciências e Tecnolgia (FCT), Universidade Nova de Lisboa (UNL), Caparica, Portugal.
| | - Roberto Larcher
- FEM-IASMA, Fondazione Edmund Mach, Istituto Agrario di San Michele all'Adige, San Michele all'Adige, TN, Italy.
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
| | - Cristina M Oliveira
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Lisbon, Portugal.
| | - Luis F Goulao
- Instituto de Investigação Científica Tropical, I.P. (IICT), Lisbon, Portugal.
- Present address: Colégio Food, Farming and Forestry, Universidade de Lisboa (ULisboa), Lisbon, Portugal.
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Pina-Martins F, Vieira BM, Seabra SG, Batista D, Paulo OS. 4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. BMC Bioinformatics 2016; 17:41. [PMID: 26787189 PMCID: PMC4719533 DOI: 10.1186/s12859-016-0892-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task. Results Here we describe 4Pipe4, a 454 data analysis pipeline particularly focused on SNP detection when no reference or strain information is available. It uses a command line interface to automatically call other programs, parse their outputs and summarize the results. The variation detection routine is built-in in the program itself. Despite being optimized for SNP mining in 454 EST data, it is flexible enough to automate the analysis of genomic data or even data from other NGS technologies. 4Pipe4 will output several HTML formatted reports with metrics on many of the most common assembly values, as well as on all the variation found. There is also a module available for finding putative SSRs in the analysed datasets. Conclusions This program can be especially useful for researchers that have 454 datasets of a panel of pooled individuals and want to discover and characterize SNPs for subsequent individual genotyping with customized genotyping arrays. In comparison with other SNP detection approaches, 4Pipe4 showed the best validation ratio, retrieving a smaller number of SNPs but with a considerably lower false positive rate than other methods. 4Pipe4’s source code is available at https://github.com/StuntsPT/4Pipe4.
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Affiliation(s)
- Francisco Pina-Martins
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal. .,Departamento de Biologia e CESAM, Univ. de Aveiro, Aveiro, Portugal.
| | - Bruno M Vieira
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Wurm Lab, School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Sofia G Seabra
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Dora Batista
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Quinta do Marquês, 2784-505, Oeiras, Portugal
| | - Octávio S Paulo
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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Róis AS, Sádio F, Paulo OS, Teixeira G, Paes AP, Espírito-Santo D, Sharbel TF, Caperta AD. Phylogeography and modes of reproduction in diploid and tetraploid halophytes of Limonium species (Plumbaginaceae): evidence for a pattern of geographical parthenogenesis. Ann Bot 2016; 117:37-50. [PMID: 26424783 PMCID: PMC4701142 DOI: 10.1093/aob/mcv138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/22/2015] [Accepted: 07/28/2015] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS The genus Limonium (Plumbaginaceae) has long been recognized to have sexual and apomictic (asexual seed formation) modes of reproduction. This study aimed to elucidate phylogeographical patterns and modes of reproduction in diploid and tetraploid Limonium species, namely three putative sexual diploid species with morphological affinities (L. nydeggeri, L. ovalifolium, L. lanceolatum) and three related, probably apomict tetraploid species (L. binervosum, L. dodartii, L. multiflorum). METHODS cpDNA diversity and differentiation between natural populations of the species were investigated using two chloroplast sequence regions (trnL intron and trnL-trnF intergenic spacer). Floral heteromorphies, ovule cytoembryological analyses and pollination and crossing tests were performed in representative species of each ploidy group, namely diploid L. ovalifolium and tetraploid L. multiflorum, using plants from greenhouse collections. KEY RESULTS AND CONCLUSIONS Genetic analyses showed that diploid species have a higher haplotype diversity and a higher number of unique (endemic) haplotypes than tetraploid species. Network analysis revealed correlations between cpDNA haplotype distribution and ploidy groups, species groups and geographical origin, and haplotype sharing within and among species with distinct ploidy levels. Reproductive biology analyses showed that diploid L. ovalifolium mainly forms meiotically reduced tetrasporic embryo sacs of Gagea ova, Adoxa and Drusa types. Limonium multiflorum, however, has only unreduced, diplosporic (apomictic) embryo sacs of Rudbeckia type, and autonomous apomictic development seems to occur. Taken together, the findings provide evidence of a pattern of 'geographical parthenogenesis' in which quaternary climatic oscillations appear to be involved in the geographical patterns of coastal diploid and tetraploid Limonium species.
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Affiliation(s)
- Ana Sofia Róis
- Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Flávio Sádio
- Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Octávio S Paulo
- cE3c - Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1649-003 Lisboa, Portugal
| | - Generosa Teixeira
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Farmácia, Universidade de Lisboa (ULisboa), Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Ana Paula Paes
- Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Dalila Espírito-Santo
- Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal, Research Network in Biodiversity and Evolutionary Biology (InBIO), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal and
| | - Timothy F Sharbel
- Apomixis Research Group, Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
| | - Ana D Caperta
- Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal, Research Network in Biodiversity and Evolutionary Biology (InBIO), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Tapada da Ajuda, 1349-017 Lisboa, Portugal and
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Ribeiro IC, Pinheiro C, Ribeiro CM, Veloso MM, Simoes-Costa MC, Evaristo I, Paulo OS, Ricardo CP. Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats. Front Plant Sci 2016; 7:1293. [PMID: 27630646 PMCID: PMC5006101 DOI: 10.3389/fpls.2016.01293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 05/20/2023]
Abstract
The establishment of stress resilient sugar beets (Beta vulgaris spp. vulgaris) is an important breeding goal since this cash crop is susceptible to drought and salinity. The genetic diversity in cultivated sugar beets is low and the beet wild relatives are useful genetic resources for tolerance traits. Three wild beet populations (Beta vulgaris spp. maritima) from contrasting environments, Vaiamonte (VMT, dry inland hill), Comporta (CMP, marsh) and Oeiras (OEI, coastland), and one commercial sugar beet (Isella variety, SB), are compared. At the genetic level, the use of six microsatellite allowed to detect a total of seventy six alleles. It was observed that CMP population has the highest value concerning the effective number of alleles and of expected heterozygosity. By contrast, sugar beet has the lowest values for all the parameters considered. Loci analysis with STRUCTURE allows defining three genetic clusters, the sea beet (OEI and CMP), the inland ruderal beet (VMT) and the sugar beet (SB). A screening test for progressive drought and salinity effects demonstrated that: all populations were able to recover from severe stress; drought impact was higher than that from salinity; the impact on biomass (total, shoot, root) was population specific. The distinct strategies were also visible at physiological level. We evaluated the physiological responses of the populations under drought and salt stress, namely at initial stress stages, late stress stages, and early stress recovery. Multivariate analysis showed that the physiological performance can be used to discriminate between genotypes, with a strong contribution of leaf temperature and leaf osmotic adjustment. However, the separation achieved and the groups formed are dependent on the stress type, stress intensity and duration. Each of the wild beet populations evaluated is very rich in genetic terms (allelic richness) and exhibited physiological plasticity, i.e., the capacity to physiologically adjust to changing environments. These characteristics emphasize the importance of the wild beet ecotypes for beet improvement programs. Two striking ecotypes are VMT, which is the best to cope with drought and salinity, and CMP which has the highest root to shoot ratio. These genotypes can supply breeding programs with distinct goals.
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Affiliation(s)
- Isa C. Ribeiro
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
- Faculdade de Ciências e Tecnologia, Universidade NOVA de LisboaCaparica, Portugal
- *Correspondence: Carla Pinheiro,
| | - Carla M. Ribeiro
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Maria M. Veloso
- INIAV, Unidade de Investigação de Biotecnologia e Recursos GenéticosOeiras, Portugal
- Instituto Superior de Agronomia, Linking Landscape, Environment, Agriculture and Food, Universidade de LisboaLisboa, Portugal
| | - Maria C. Simoes-Costa
- Instituto Superior de Agronomia, Linking Landscape, Environment, Agriculture and Food, Universidade de LisboaLisboa, Portugal
| | - Isabel Evaristo
- INIAV, Unidade de Investigação de Sistemas Agrários e Florestais e Sanidade VegetalOeiras, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Cândido P. Ricardo
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de LisboaOeiras, Portugal
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Silva DN, Duplessis S, Talhinhas P, Azinheira H, Paulo OS, Batista D. Genomic Patterns of Positive Selection at the Origin of Rust Fungi. PLoS One 2015; 10:e0143959. [PMID: 26632820 PMCID: PMC4669144 DOI: 10.1371/journal.pone.0143959] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/11/2015] [Indexed: 01/24/2023] Open
Abstract
Understanding the origin and evolution of pathogenicity and biotrophic life-style of rust fungi has remained a conundrum for decades. Research on the molecular mechanisms responsible for rust fungi evolution has been hampered by their biotrophic life-style until the sequencing of some rust fungi genomes. With the availability of multiple whole genomes and EST data for this group, it is now possible to employ genome-wide surveys and investigate how natural selection shaped their evolution. In this work, we employed a phylogenomics approach to search for positive selection and genes undergoing accelerated evolution at the origin of rust fungi on an assembly of single copy genes conserved across a broad range of basidiomycetes. Up to 985 genes were screened for positive selection on the phylogenetic branch leading to rusts, revealing a pervasive signal of positive selection throughout the data set with the proportion of positively selected genes ranging between 19.6–33.3%. Additionally, 30 genes were found to be under accelerated evolution at the origin of rust fungi, probably due to a mixture of positive selection and relaxation of purifying selection. Functional annotation of the positively selected genes revealed an enrichment in genes involved in the biosynthesis of secondary metabolites and several metabolism and transporter classes.
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Affiliation(s)
- Diogo N. Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- Computational Biology and Population Genomics group, cE3c – Centre for Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Departamento de Biologia e CESAM – Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
- * E-mail:
| | - Sebastien Duplessis
- Institut National de la Recherche Agronomique, UMR 1136 INRA/Université de Lorraine Interactions Arbres-Microorganismes, Champenoux, France
- Université de Lorraine, UMR 1136, INRA/Université de Lorraine Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Pedro Talhinhas
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Helena Azinheira
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics group, cE3c – Centre for Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Dora Batista
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
- Computational Biology and Population Genomics group, cE3c – Centre for Centre for Ecology Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
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Seabra SG, Satar I, Paulo OS. Microsatellite loci isolated from Chamaeleo chamaeleon. J Genet 2014; 93:e144-e147. [PMID: 25572071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Sofia G Seabra
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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Seabra SG, Brás PG, Martins J, Martins R, Wyatt N, Shirazi J, Rebelo MT, Franco JC, Mateus C, Figueiredo E, Paulo OS. Phylogeographical patterns inCoenosia attenuata(Diptera: Muscidae): a widespread predator of insect species associated with greenhouse crops. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sofia G. Seabra
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Patrícia G. Brás
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Joana Martins
- Centro de Engenharia dos Biossistemas; Instituto Superior de Agronomia; Universidade de Lisboa; Tapada da Ajuda 1349-017 Lisboa Portugal
| | - Renata Martins
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Nigel Wyatt
- Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Jalal Shirazi
- Biocontrol Research Department; Iranian Research Institute of Plant Protection (IRIPP); PO Box 1454 Tehran 19395 Iran
| | - Maria Teresa Rebelo
- Centro de Estudos do Ambiente e do Mar (CESAM); Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - José Carlos Franco
- Centro de Estudos Florestais; Instituto Superior de Agronomia; Universidade de Lisboa; Tapada da Ajuda 1349-017 Lisboa Portugal
| | - Célia Mateus
- Instituto Nacional de Investigação Agrária e Veterinária; Av. República Quinta do Marquês 2784-505 Oeiras Portugal
| | - Elisabete Figueiredo
- Centro de Engenharia dos Biossistemas; Instituto Superior de Agronomia; Universidade de Lisboa; Tapada da Ajuda 1349-017 Lisboa Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes; Departamento de Biologia Animal; Faculdade de Ciências; Universidade de Lisboa; 1749-016 Lisboa Portugal
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Simões PC, Nunes VL, Mendes R, Seabra SG, Paulo OS, Quartau JA. Tettigettalnajosei (Boulard, 1982) (Hemiptera: Cicadoidea): first record in Spain, with notes on the distribution, genetic variation and behaviour of the species. Biodivers Data J 2014:e1045. [PMID: 24891819 PMCID: PMC4040400 DOI: 10.3897/bdj.2.e1045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/06/2014] [Indexed: 11/22/2022] Open
Abstract
The small cicada Tettigettalnajosei (Boulard, 1982) was until recently only known from southern Portugal and was considered endemic to this country. Fieldwork in 2013 led to the first record of the species in Spain, expanding its known eastern range to Andalusia. The northern limits remain poorly defined but it appears that the distribution of Tettigettalnajosei is restricted to the south Atlantic coastline in the Iberian Peninsula, with the highest densities found in Algarve. Some notes on behaviour and genetic variation of Tettigettalnajosei are also given.
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Affiliation(s)
- Paula C Simões
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Edifício C2, Piso 3, Campo Grande, 1749-016, Lisbon, Portugal
| | - Vera L Nunes
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Edifício C2, Piso 3, Campo Grande, 1749-016, Lisbon, Portugal
| | - Raquel Mendes
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Edifício C2, Piso 3, Campo Grande, 1749-016, Lisbon, Portugal
| | - Sofia G Seabra
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Edifício C2, Piso 3, Campo Grande, 1749-016, Lisbon, Portugal
| | - Octávio S Paulo
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Edifício C2, Piso 3, Campo Grande, 1749-016, Lisbon, Portugal
| | - José A Quartau
- Faculdade de Ciências da Universidade de Lisboa, Departamento de Biologia Animal e Centro de Biologia Ambiental, Computational Biology and Population Genomics Group, Edifício C2, Piso 3, Campo Grande, 1749-016, Lisbon, Portugal
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Rodrigues ASB, Silva SE, Marabuto E, Silva DN, Wilson MR, Thompson V, Yurtsever S, Halkka A, Borges PAV, Quartau JA, Paulo OS, Seabra SG. New mitochondrial and nuclear evidences support recent demographic expansion and an atypical phylogeographic pattern in the spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae). PLoS One 2014; 9:e98375. [PMID: 24892429 PMCID: PMC4043774 DOI: 10.1371/journal.pone.0098375] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Philaenus spumarius is a widespread insect species in the Holarctic region. Here, by focusing on the mtDNA gene COI but also using the COII and Cyt b genes and the nuclear gene EF-1α, we tried to explain how and when its current biogeographic pattern evolved by providing time estimates of the main demographic and evolutionary events and investigating its colonization patterns in and out of Eurasia. Evidence of recent divergence and expansion events at less than 0.5 Ma ago indicate that climate fluctuations in the Mid-Late Pleistocene were important in shaping the current phylogeographic pattern of the species. Data support a first split and differentiation of P. spumarius into two main mitochondrial lineages: the "western", in the Mediterranean region and the "eastern", in Anatolia/Caucasus. It also supports a following differentiation of the "western" lineage into two sub-lineages: the "western-Mediterranean", in Iberia and the "eastern-Mediterranean" in the Balkans. The recent pattern seems to result from postglacial range expansion from Iberia and Caucasus/Anatolia, thus not following one of the four common paradigms. Unexpected patterns of recent gene-flow events between Mediterranean peninsulas, a close relationship between Iberia and North Africa, as well as high levels of genetic diversity being maintained in northern Europe were found. The mitochondrial pattern does not exactly match to the nuclear pattern suggesting that the current biogeographic pattern of P. spumarius may be the result of both secondary admixture and incomplete lineage sorting. The hypothesis of recent colonization of North America from both western and northern Europe is corroborated by our data and probably resulted from accidental human translocations. A probable British origin for the populations of the Azores and New Zealand was revealed, however, for the Azores the distribution of populations in high altitude native forests is somewhat puzzling and may imply a natural colonization of the archipelago.
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Affiliation(s)
- Ana S. B. Rodrigues
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sara E. Silva
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Eduardo Marabuto
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Diogo N. Silva
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mike R. Wilson
- Department of Natural Sciences, National Museum of Wales, Cardiff, United Kingdom
| | - Vinton Thompson
- Metropolitan College of New York, New York, New York, United States of America
| | - Selçuk Yurtsever
- Biology Department, Science Faculty, Trakya University, Edirne, Turkey
| | - Antti Halkka
- Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Paulo A. V. Borges
- Azorean Biodiversity Group, Centro de Investigação e Tecnologias Agrárias dos Açores and Platform for Enhancing Ecological Research & Sustainability, Universidade dos Açores, Departamento de Ciências Agrárias, Angra do Heroísmo, Terceira, Portugal
| | - José A. Quartau
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sofia G. Seabra
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal/Platform for Enhancing Ecological Research & Sustainability, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Sebastiana M, Vieira B, Lino-Neto T, Monteiro F, Figueiredo A, Sousa L, Pais MS, Tavares R, Paulo OS. Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling. PLoS One 2014; 9:e98376. [PMID: 24859293 PMCID: PMC4032270 DOI: 10.1371/journal.pone.0098376] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the "symbiosis toolkits" and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19,552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.
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Affiliation(s)
- Mónica Sebastiana
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Bruno Vieira
- Center for Environmental Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Teresa Lino-Neto
- Plant Functional Biology Centre, Center for Biodiversity, Functional and Integrative Genomics, University of Minho, Braga, Portugal
| | - Filipa Monteiro
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Andreia Figueiredo
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Lisete Sousa
- Department of Statistics and Operational Research, Center of Statistics and Applications from Lisbon University, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Maria Salomé Pais
- Plant Systems Biology Lab, Center for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Rui Tavares
- Plant Functional Biology Centre, Center for Biodiversity, Functional and Integrative Genomics, University of Minho, Braga, Portugal
| | - Octávio S. Paulo
- Center for Environmental Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Pereira-Leal JB, Abreu IA, Alabaça CS, Almeida MH, Almeida P, Almeida T, Amorim MI, Araújo S, Azevedo H, Badia A, Batista D, Bohn A, Capote T, Carrasquinho I, Chaves I, Coelho AC, Costa MMR, Costa R, Cravador A, Egas C, Faro C, Fortes AM, Fortunato AS, Gaspar MJ, Gonçalves S, Graça J, Horta M, Inácio V, Leitão JM, Lino-Neto T, Marum L, Matos J, Mendonça D, Miguel A, Miguel CM, Morais-Cecílio L, Neves I, Nóbrega F, Oliveira MM, Oliveira R, Pais MS, Paiva JA, Paulo OS, Pinheiro M, Raimundo JAP, Ramalho JC, Ribeiro AI, Ribeiro T, Rocheta M, Rodrigues AI, Rodrigues JC, Saibo NJM, Santo TE, Santos AM, Sá-Pereira P, Sebastiana M, Simões F, Sobral RS, Tavares R, Teixeira R, Varela C, Veloso MM, Ricardo CPP. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics 2014; 15:371. [PMID: 24885229 PMCID: PMC4070548 DOI: 10.1186/1471-2164-15-371] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/15/2014] [Indexed: 01/17/2023] Open
Abstract
Background Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.
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Affiliation(s)
- José B Pereira-Leal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2780-156, Portugal.
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Talhinhas P, Azinheira HG, Vieira B, Loureiro A, Tavares S, Batista D, Morin E, Petitot AS, Paulo OS, Poulain J, Da Silva C, Duplessis S, Silva MDC, Fernandez D. Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection. Front Plant Sci 2014; 5:88. [PMID: 24672531 PMCID: PMC3953675 DOI: 10.3389/fpls.2014.00088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 02/24/2014] [Indexed: 05/06/2023]
Abstract
Hemileia vastatrix is the causal agent of coffee leaf rust, the most important disease of coffee Arabica. In this work, a 454-pyrosequencing transcriptome analysis of H. vastatrix germinating urediniospores (gU) and appressoria (Ap) was performed and compared to previously published in planta haustoria-rich (H) data. A total of 9234 transcripts were identified and annotated. Ca. 50% of these transcripts showed no significant homology to international databases. Only 784 sequences were shared by the three conditions, and 75% were exclusive of either gU (2146), Ap (1479) or H (3270). Relative transcript abundance and RT-qPCR analyses for a selection of genes indicated a particularly active metabolism, translational activity and production of new structures in the appressoria and intense signaling, transport, secretory activity and cellular multiplication in the germinating urediniospores, suggesting the onset of a plant-fungus dialogue as early as at the germ tube stage. Gene expression related to the production of carbohydrate-active enzymes and accumulation of glycerol in germinating urediniospores and appressoria suggests that combined lytic and physical mechanisms are involved in appressoria-mediated penetration. Besides contributing to the characterization of molecular processes leading to appressoria-mediated infection by rust fungi, these results point toward the identification of new H. vastatrix candidate virulence factors, with 516 genes predicted to encode secreted proteins.
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Affiliation(s)
- Pedro Talhinhas
- Centro de Investigação das Ferrugens do Cafeeiro/BioTrop/Instituto de Investigação Científica TropicalOeiras, Portugal
| | - Helena G. Azinheira
- Centro de Investigação das Ferrugens do Cafeeiro/BioTrop/Instituto de Investigação Científica TropicalOeiras, Portugal
| | - Bruno Vieira
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Andreia Loureiro
- Centro de Investigação das Ferrugens do Cafeeiro/BioTrop/Instituto de Investigação Científica TropicalOeiras, Portugal
| | - Sílvia Tavares
- Centro de Investigação das Ferrugens do Cafeeiro/BioTrop/Instituto de Investigação Científica TropicalOeiras, Portugal
| | - Dora Batista
- Centro de Investigação das Ferrugens do Cafeeiro/BioTrop/Instituto de Investigação Científica TropicalOeiras, Portugal
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, Centre INRA Nancy Lorraine, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Micro-organismesChampenoux, France
- Université de Lorraine, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Micro-organismes, Faculté des Sciences et TechnologiesVandoeuvre-lès-Nancy, France
| | - Anne-Sophie Petitot
- Institut de Recherche pour le Développement, UMR 186 IRD-Cirad-UM2 Résistance des Plantes aux BioagresseursMontpellier, France
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de LisboaLisboa, Portugal
| | - Julie Poulain
- Genoscope, Centre National de Séquençage, Commissariat à l'Energie Atomique, Institut de GénomiqueEvry, France
| | - Corinne Da Silva
- Genoscope, Centre National de Séquençage, Commissariat à l'Energie Atomique, Institut de GénomiqueEvry, France
| | - Sébastien Duplessis
- Institut National de la Recherche Agronomique, Centre INRA Nancy Lorraine, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Micro-organismesChampenoux, France
- Université de Lorraine, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Micro-organismes, Faculté des Sciences et TechnologiesVandoeuvre-lès-Nancy, France
| | - Maria do Céu Silva
- Centro de Investigação das Ferrugens do Cafeeiro/BioTrop/Instituto de Investigação Científica TropicalOeiras, Portugal
| | - Diana Fernandez
- Institut de Recherche pour le Développement, UMR 186 IRD-Cirad-UM2 Résistance des Plantes aux BioagresseursMontpellier, France
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Nunes VL, Mendes R, Marabuto E, Novais BM, Hertach T, Quartau JA, Seabra SG, Paulo OS, Simões PC. Conflicting patterns of DNA barcoding and taxonomy in the cicada genus Tettigettalna from Southern Europe (Hemiptera: Cicadidae). Mol Ecol Resour 2013; 14:27-38. [PMID: 24034529 DOI: 10.1111/1755-0998.12158] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/16/2013] [Accepted: 07/31/2013] [Indexed: 02/02/2023]
Abstract
DNA barcodes have great potential to assist in species identification, especially when high taxonomical expertise is required. We investigated the utility of the 5' mitochondrial cytochrome c oxidase I (COI) region to discriminate between 13 European cicada species. These included all nine species currently recognized under the genus Tettigettalna, from which seven are endemic to the southern Iberian Peninsula. These cicadas have species-specific male calling songs but are morphologically very similar. Mean COI divergence between congeners ranged from 0.4% to 10.6%, but this gene was proven insufficient to determine species limits within genus Tettigettalna because a barcoding gap was absent for several of its species, that is, the highest intraspecific distance exceeded the lowest interspecific distance. The genetic data conflicted with current taxonomic classification for T. argentata and T. mariae. Neighbour-joining and Bayesian analyses revealed that T. argentata is geographically structured (clades North and South) and might constitute a species complex together with T. aneabi and T. mariae. The latter diverges very little from the southern clade of T. argentata and shares with it its most common haplotype. T. mariae is often in sympatry with T. argentata but it remains unclear whether introgression or incomplete lineage sorting may be responsible for the sharing of haplotypes. T. helianthemi and T. defauti also show high intraspecific variation that might signal hidden cryptic diversity. These taxonomic conflicts must be re-evaluated with further studies using additional genes and extensive morphological and acoustic analyses.
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Affiliation(s)
- Vera L Nunes
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, DBA/FCUL, Lisboa, 1749-016, Portugal
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Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2013; 2:10. [PMID: 23870653 PMCID: PMC3844414 DOI: 10.1186/2047-217x-2-10] [Citation(s) in RCA: 415] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. RESULTS In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. CONCLUSIONS Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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Seabra SG, Brás PG, Zina V, Borges da Silva E, Rebelo MT, Figueiredo E, Mendel Z, Paulo OS, Franco JC. Molecular evidence of polyandry in the citrus mealybug, Planococcus citri (Hemiptera: Pseudococcidae). PLoS One 2013; 8:e68241. [PMID: 23844173 PMCID: PMC3700894 DOI: 10.1371/journal.pone.0068241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/28/2013] [Indexed: 11/18/2022] Open
Abstract
The occurrence of polyandry in Planococcuscitri, presumed by earlier observations of mating behavior, was confirmed using microsatellite genotyping of pools of over 400 eggs resulting from controlled crosses of one female with two males. The genetic contribution of both mated males was confirmed in 13 out of 43 crosses. In three crosses it was possible to determine that only the first male fertilized the eggs, which may be due to sperm competition or unviable sperm supply. The microsatellite analysis also allowed the confirmation of aspects of the chromosomal inheritance detected previously in cytogenetic studies in Planococcuscitri, namely that only one of the alleles is transmitted by the male, indicating that the males are functionally haploid, supporting the observation of Paternal Genome Elimination (PGE) in these insects.
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Affiliation(s)
- Sofia G Seabra
- Computational Biology and Population Genomics Group, Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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50
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Silva SE, Silva IC, Madeira C, Sallema R, Paulo OS, Paula J. Genetic and morphological variation in two littorinid gastropods: evidence for recent population expansions along the East African coast. Biol J Linn Soc Lond 2013. [DOI: 10.1111/j.1095-8312.2012.02041.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sara E. Silva
- Computational Biology and Population Genomics Group; Centro de Biologia Ambiental; Departamento de Biologia Animal; Faculdade de Ciências da Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - Inês C. Silva
- Centro de Oceanografia; Laboratório Marítimo da Guia; Faculdade de Ciências da Universidade de Lisboa; 2750-374 Cascais Portugal
| | - Carolina Madeira
- Centro de Oceanografia; Laboratório Marítimo da Guia; Faculdade de Ciências da Universidade de Lisboa; 2750-374 Cascais Portugal
| | - Rose Sallema
- National Environment Management Council; PO Box 63154 Dar es Salaam Tanzania
| | - Octávio S. Paulo
- Computational Biology and Population Genomics Group; Centro de Biologia Ambiental; Departamento de Biologia Animal; Faculdade de Ciências da Universidade de Lisboa; 1749-016 Lisboa Portugal
| | - José Paula
- Centro de Oceanografia; Laboratório Marítimo da Guia; Faculdade de Ciências da Universidade de Lisboa; 2750-374 Cascais Portugal
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