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Zhang S, Gao X, Wang L, Jiang W, Su H, Jing T, Cui J, Zhang L, Yang Y. Chromosome-level genome assemblies of two cotton-melon aphid Aphis gossypii biotypes unveil mechanisms of host adaption. Mol Ecol Resour 2021; 22:1120-1134. [PMID: 34601821 DOI: 10.1111/1755-0998.13521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/30/2022]
Abstract
The cotton-melon aphid Aphis gossypii is a sap-sucking insect that is considered a serious global pest. The species is distributed over a large geographical range and uses a wide variety of hosts, with some populations being specialized to attack different plant species. Here, we provide de novo chromosome-level genome assemblies of a cotton specialist population (Hap1) and a cucurbit specialist population (Hap3). We achieved this by using a combination of third-generation sequencing platforms, namely Illumina and Hi-C sequencing technologies. We were able to anchor a total of 334.89 Mb (scaffold N50 of 89.13 Mb) and 359.95 Mb (scaffold N50 of 68.88 Mb) to four chromosomes for Hap1 and Hap3, respectively. Moreover, our results showed that the X-chromosome of Hap3 (113.01 Mb) was significantly longer than that of Hap1 (100.26 Mb), with a high level of sequence conservation between the aphid species. We also report variation in the number of protein-coding genes and repeat sequences between Hap1 and Hap3. In particular, olfactory and gustatory receptor genes underwent a high level of gene duplication and expansion events in A. gossypii, including between Hap1 and Hap3. Moreover, we identified two glutathione S-transferase genes which underwent single gene duplications in Hap3, and tandem duplication and inversion events affecting the cytochrome P450 monooxygenase between Hap1 and Hap3, all of which include the CYP3 family. Our results illustrate the variance in the genomic composition of two specialized A. gossypii populations and provide a helpful resource for the study of aphid population evolution, host adaption and insecticide resistance.
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Affiliation(s)
- Shuai Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xueke Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Weili Jiang
- Basic Experimental Teaching Center of Life Sciences, Yangzhou University, Yangzhou, China
| | - Honghua Su
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Tianxing Jing
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Jinjie Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lijuan Zhang
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yizhong Yang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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2
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Chen C, Zhu H, Li SY, Han YY, Chen L, Fan BQ, Zhang YF, Wang Y, Hao DJ. Insights into chemosensory genes of Pagiophloeus tsushimanus adults using transcriptome and qRT-PCR analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 37:100785. [PMID: 33548831 DOI: 10.1016/j.cbd.2020.100785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 11/18/2022]
Abstract
Pagiophloeus tsushimanus is a new, destructive, and monophagous weevil pest that thrives on Cinnamomum camphora, found in Shanghai. The functions of chemosensory genes involved in the host location and intraspecific communication of P. tsushimanus remain unknown. The male-female transcriptomes of P. tsushimanus adults were assembled using Illumina sequencing, and we focused on all chemosensory genes in transcriptomes. In general, 58,088 unigenes with a mean length of 1018.19 bp were obtained. In total, 39 odorant binding proteins (OBPs), 10 chemosensory proteins (CSPs), 22 olfactory receptors (ORs), 16 gustatory receptors (GRs), eight ionotropic receptors (IRs), and five sensory neuron membrane proteins (SNMPs) were identified. PtsuOBPs comprised four subfamilies (20 Minus-C, one Plus-C, two Dimer, and 15 Classic). Both PtsuOBPs and PtsuCSPs contained a highly conserved sequence motif of cysteine residues. PtsuORs including one olfactory receptor co-receptors (Ptsu/Orco) comprised seven predicted transmembrane domains. Phylogenetic analysis revealed that PtsuOBPs, PtsuCSPs, and PtsuORs in P. tsushimanus exhibited low homology compared to other insect species. The results of tissue- and sex-specific expression patterns indicated that PtsuOBPs and PtsuORs were highly abundant in the antennae; whereas, PtsuCSPs were not only highly abundant in antennae, but also abdominal apexes, wings, and legs. In conclusion, these results enrich the gene database of P. tsushimanus, which may serve as a basis for identifying novel targets to disrupt olfactory key genes and may provide a reverse validation method to identify attractants for formulating potential eco-friendly control strategies for this pest.
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Affiliation(s)
- Cong Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China; College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Han Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China; College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Shou-Yin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China; College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Liang Chen
- Shanghai Kaisheng Landscape Engineering Co., Ltd, Shanghai, China
| | - Bin-Qi Fan
- Forest Station of Shanghai, Shanghai, China
| | | | - Yan Wang
- Forest Station of Shanghai, Shanghai, China
| | - De-Jun Hao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China; College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China.
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3
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Badji CA, Sol-Mochkovitch Z, Fallais C, Sochard C, Simon JC, Outreman Y, Anton S. Alarm Pheromone Responses Depend on Genotype, but Not on the Presence of Facultative Endosymbionts in the Pea Aphid Acyrthosiphon pisum. INSECTS 2021; 12:43. [PMID: 33430009 PMCID: PMC7826508 DOI: 10.3390/insects12010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022]
Abstract
Aphids use an alarm pheromone, E-β farnesene (EBF), to warn conspecifics of potential danger. The antennal sensitivity and behavioural escape responses to EBF can be influenced by different factors. In the pea aphid, Acyrthosiphon pisum, different biotypes are adapted to different legume species, and within each biotype, different genotypes exist, which can carry or not Hamiltonella defensa, a bacterial symbiont that can confer protection against natural enemies. We investigate here the influence of the aphid genotype and symbiotic status on the escape behaviour using a four-way olfactometer and antennal sensitivity for EBF using electroantennograms (EAGs). Whereas the investigated three genotypes from two biotypes showed significantly different escape and locomotor behaviours in the presence of certain EBF doses, the infection with H. defensa did not significantly modify the escape behaviour and only marginally influenced the locomotor behaviour at high doses of EBF. Dose-response curves of EAG amplitudes after stimulation with EBF differed significantly between aphid genotypes in correlation with behavioural differences, whereas antennal sensitivity to EBF did not change significantly as a function of the symbiotic status. The protective symbiont H. defensa does thus not modify the olfactory sensitivity to the alarm pheromone. How EBF sensitivity is modified between genotypes or biotypes remains to be investigated.
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Affiliation(s)
- Cesar Auguste Badji
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
| | - Zoé Sol-Mochkovitch
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
| | - Charlotte Fallais
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
| | - Corentin Sochard
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 35000 Rennes, France; (C.S.); (Y.O.)
| | | | - Yannick Outreman
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 35000 Rennes, France; (C.S.); (Y.O.)
| | - Sylvia Anton
- IGEPP, INRAE, Institut Agro, University Rennes, CEDEX, 49045 Angers, France; (C.A.B.); (Z.S.-M.); (C.F.)
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4
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Gallardo-Escárate C, Valenzuela-Muñoz V, Núñez-Acuña G, Carrera C, Gonçalves AT, Valenzuela-Miranda D, Benavente BP, Roberts S. Catching the complexity of salmon-louse interactions. FISH & SHELLFISH IMMUNOLOGY 2019; 90:199-209. [PMID: 31048036 DOI: 10.1016/j.fsi.2019.04.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The study of host-parasite relationships is an integral part of the immunology of aquatic species, where the complexity of both organisms has to be overlayed with the lifecycle stages of the parasite and immunological status of the host. A deep understanding of how the parasite survives in its host and how they display molecular mechanisms to face the immune system can be applied for novel parasite control strategies. This review highlights current knowledge about salmon and sea louse, two key aquatic animals for aquaculture research worldwide. With the aim to catch the complexity of the salmon-louse interactions, molecular information gleaned through genomic studies are presented. The host recognition system and the chemosensory receptors found in sea lice reveal complex molecular components, that in turn, can be disrupted through specific molecules such as non-coding RNAs.
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Affiliation(s)
- Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile.
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Gustavo Núñez-Acuña
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Crisleri Carrera
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Ana Teresa Gonçalves
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Bárbara P Benavente
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, USA
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Robertson HM, Robertson ECN, Walden KKO, Enders LS, Miller NJ. The chemoreceptors and odorant binding proteins of the soybean and pea aphids. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 105:69-78. [PMID: 30654011 DOI: 10.1016/j.ibmb.2019.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
We examined the genome of the soybean aphid, Aphis glycines, and an updated genome assembly of the pea aphid, Acyrthosiphon pisum, for members of the three major families of chemoreceptors, the Odorant Receptors (ORs), Gustatory Receptors (GRs) and Ionotropic Receptors (IRs), as well as the Odorant Binding Proteins (OBPs). The soybean aphid has 47 ORs, 61 GRs, 19 IRs, and 10 OBPs, compared with 87 ORs, 78 Grs, 19 IRs, and 18 OBPs in the pea aphid, with variable numbers of pseudogenes in the OR and GR families. Phylogenetic analysis reveals that while all of the IRs are simple orthologs between these two species, the OR, GR, and OBP families in the pea aphid have experienced major expansions of particular gene lineages and fewer losses of gene lineages. This imbalance in birth-and-death of chemosensory genes has led to the larger pea aphid gene repertoire, which might be related to the broader host range of pea aphids versus the specialization of soybean aphids on a single summer host plant. Examination of the expression levels of these chemosensory genes in parthenogenetic and sexual females and males of pea aphids revealed multiple genes that are differentially expressed in sexual females or males and might be involved in reproductive biology. Examination of the soybean aphid genes in parthenogenetic females under multiple stressors revealed multiple genes whose expression levels changed with heat or starvation stress, the latter potentially important in finding new food sources.
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Affiliation(s)
- Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Erica C N Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Laramy S Enders
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
| | - Nicholas J Miller
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA.
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6
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Doellman MM, Feder JL. Genomic transitions during host race and species formation. CURRENT OPINION IN INSECT SCIENCE 2019; 31:84-92. [PMID: 31109679 DOI: 10.1016/j.cois.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Darwin recognized species as discontinuous, yet considered them to be formed by an incremental process of natural selection. Recent theoretical work on 'genome-wide congealing' is bridging this gap between the gradualism of divergent selection and rapid genome-wide divergence, particularly during ecological speciation-with-gene-flow. Host races and species of phytophagous insects, displaying a spectrum of divergence and gene flow among member taxa, provide model systems for testing predicted non-linear transitions from 'genic' divergence at a few uncoupled loci to 'genomic' divergence with genome-wide coupling of selected loci and strong reproductive isolation. Integrating across natural history, genomics, and evolutionary theory, emerging research suggests a tipping point from 'genic' to 'genomic' divergence between host races and species, during both sympatric speciation and secondary contact.
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Affiliation(s)
- Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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7
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Fazalova V, Nevado B, McLean A, Godfray HCJ. Intrinsic pre-zygotic reproductive isolation of distantly related pea aphid host races. Biol Lett 2018; 14:rsbl.2018.0332. [PMID: 30487255 DOI: 10.1098/rsbl.2018.0332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 12/23/2022] Open
Abstract
Human activities may weaken or destroy reproductive isolation between young taxa, leading to their fusion with consequences for population and community ecology. Pea aphid host races are adapted to different legume taxa, providing a degree of pre-mating isolation mediated by habitat choice. Yet, all races can feed and reproduce on the broad bean (Vicia faba), a major crop which represents a 'universal host plant', which can promote hybridization between races. Here, we ask if pea aphid host races have reproductive barriers which prevent or reduce gene flow when they co-occur on the universal host plant. We observed mating behaviour, female survival, number of eggs and egg fertilization rates for three types of crosses: among individuals of the same host race, between closely related host races and between distantly related host races. We did not find significant differences in mating behaviour and female survival among the three types of crosses. However, we observed a drastic reduction in the number of eggs laid, and in the number of fertilized eggs, in distant crosses. We conclude that widespread broad bean cultivation in agriculture may predispose closely related-but not distantly related-host races to hybridize, disrupting reproductive isolation between incipient species.
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Affiliation(s)
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ailsa McLean
- Department of Zoology, University of Oxford, Oxford, UK
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8
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Wen X, Wang Q, Gao P, Wen J. Identification and Comparison of Chemosensory Genes in the Antennal Transcriptomes of Eucryptorrhynchus scrobiculatus and E. brandti Fed on Ailanthus altissima. Front Physiol 2018; 9:1652. [PMID: 30515106 PMCID: PMC6256065 DOI: 10.3389/fphys.2018.01652] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
The key to the coexistence of two or more species on the same host is ecological niche separation. Adult Eucryptorrhynchus scrobiculatus and E. brandti both feed on the tree of heaven, Ailanthus altissima, but on different sections of the plant. Olfaction plays a vital role in foraging for food resources. Chemosensory genes on the antennae, the main organ for insect olfaction, might explain their feeding differentiation. In the present study, we identified 130 and 129 putative chemosensory genes in E. scrobiculatus and E. brandti, respectively, by antennal transcriptome sequencing, including 31 odorant-binding proteins (OBPs), 11 chemosensory proteins (CSPs), 49 odorant receptors (ORs), 17 ionotropic receptors (IRs), 19 gustatory receptors (GRs), and three sensory neuron membrane proteins (SNMPs) in E. scrobiculatus and 28 OBPs, 11 CSPs, 45 ORs, 25 IRs, 17 GRs, and three SNMPs in E. brandti. We inferred that EscrOBP8 (EscrPBP1), EscrOBP24 (EscrPBP2) and EbraOBP8 (EbraPBP1), EbraOBP24 (EbraPBP2) were putative PBPs by the phylogenetic analysis. We identified species-specific OR transcripts (10 EscrORs and 8 EbraORs) with potential roles in the recognition of specific volatiles of A. altissima. In addition to conserved “antennal IRs,” we also found several “divergent IRs” orthologues in E. scrobiculatus and E. brandti, such as EscrIR16, EbraIR19, and EbraIR20. Compared with other chemosensory genes, GRs between E. scrobiculatus and E. brandti shared lower amino acid identities, which could explain the different feeding habits of the species. We examined OBP expression patterns in various tissues and sexes. Although amino acid sequence similarities were high between EscrOBPs and EbraOBPs, the homologous OBPs showed different tissue expression pattern between two weevils. Our systematic comparison of chemosensory genes in E. scrobiculatus and E. brandti provides a foundation for studies of olfaction and olfactory differentiation in the two weevils as well as a theoretical basis for studying species differentiation.
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Affiliation(s)
- Xiaojian Wen
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Qian Wang
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Peng Gao
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Junbao Wen
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
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9
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Boulain H, Legeai F, Guy E, Morlière S, Douglas NE, Oh J, Murugan M, Smith M, Jaquiéry J, Peccoud J, White FF, Carolan JC, Simon JC, Sugio A. Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants. Genome Biol Evol 2018; 10:1554-1572. [PMID: 29788052 PMCID: PMC6012102 DOI: 10.1093/gbe/evy097] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/31/2022] Open
Abstract
Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in comparison to the alimentary tract. A search for orthologs in 17 arthropod genomes revealed that SG-up-regulated effector candidates of A. pisum are enriched in aphid-specific genes and tend to evolve faster compared with the whole gene set. We also found that a large fraction of proteins detected in the A. pisum saliva belonged to three gene families, of which certain members show evidence consistent with positive selection. Overall, this comprehensive analysis suggests that the large repertoire of effector candidates in A. pisum constitutes a source of novelties promoting plant adaptation to legumes.
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Affiliation(s)
- Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France.,Inria/IRISA GenScale, Campus de Beaulieu, Rennes, France
| | - Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Nadine E Douglas
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,UCD School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Marimuthu Murugan
- Community Science College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Michael Smith
- Department of Entomology, Kansas State University, Manhattan, Kansas
| | - Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, équipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, Florida
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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10
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The Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 is a molecular host-associated cue for the salmon louse (Lepeophtheirus salmonis). Sci Rep 2018; 8:13738. [PMID: 30213966 PMCID: PMC6137231 DOI: 10.1038/s41598-018-31885-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/28/2018] [Indexed: 01/02/2023] Open
Abstract
Chemical signals are a key element of host-parasite interactions. In marine ecosystems, obligate ectoparasites, such as sea lice, use chemical cues and other sensory signals to increase the probability of encountering a host and to identify appropriate hosts on which they depend to complete their life cycle. The chemical compounds that underlie host identification by the sea lice are not fully described or characterized. Here, we report a novel compound - the Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 (Cath-2) – that acts as an activation cue for the marine parasitic copepod Lepeophtheirus salmonis. L. salmonis were exposed to 0, 7, 70 and 700 ppb of Cath-2 and neural activity, swimming behaviour and gene expression profiles of animals in response to the peptide were evaluated. The neurophysiological, behavioural and transcriptomic results were consistent: L. salmonis detects Cath-2 as a water-soluble peptide released from the skin of salmon, triggering chemosensory neural activity associated with altered swimming behaviour of copepodids exposed to the peptide, and chemosensory-related genes were up-regulated in copepodids exposed to the peptide. L. salmonis are activated by Cath-2, indicating a tight link between this peptide and the salmon louse chemosensory system.
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11
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Blaazer CJH, Villacis-Perez EA, Chafi R, Van Leeuwen T, Kant MR, Schimmel BCJ. Why Do Herbivorous Mites Suppress Plant Defenses? FRONTIERS IN PLANT SCIENCE 2018; 9:1057. [PMID: 30105039 PMCID: PMC6077234 DOI: 10.3389/fpls.2018.01057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 06/28/2018] [Indexed: 05/03/2023]
Abstract
Plants have evolved numerous defensive traits that enable them to resist herbivores. In turn, this resistance has selected for herbivores that can cope with defenses by either avoiding, resisting or suppressing them. Several species of herbivorous mites, such as the spider mites Tetranychus urticae and Tetranychus evansi, were found to maximize their performance by suppressing inducible plant defenses. At first glimpse it seems obvious why such a trait will be favored by natural selection. However, defense suppression appeared to readily backfire since mites that do so also make their host plant more suitable for competitors and their offspring more attractive for natural enemies. This, together with the fact that spider mites are infamous for their ability to resist (plant) toxins directly, justifies the question as to why traits that allow mites to suppress defenses nonetheless seem to be relatively common? We argue that this trait may facilitate generalist herbivores, like T. urticae, to colonize new host species. While specific detoxification mechanisms may, on average, be suitable only on a narrow range of similar hosts, defense suppression may be more broadly effective, provided it operates by targeting conserved plant signaling components. If so, resistance and suppression may be under frequency-dependent selection and be maintained as a polymorphism in generalist mite populations. In that case, the defense suppression trait may be under rapid positive selection in subpopulations that have recently colonized a new host but may erode in relatively isolated populations in which host-specific detoxification mechanisms emerge. Although there is empirical evidence to support these scenarios, it contradicts the observation that several of the mite species found to suppress plant defenses actually are relatively specialized. We argue that in these cases buffering traits may enable such mites to mitigate the negative side effects of suppression in natural communities and thus shield this trait from natural selection.
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Affiliation(s)
- C. Joséphine H. Blaazer
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ernesto A. Villacis-Perez
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Rachid Chafi
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Thomas Van Leeuwen
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Merijn R. Kant
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Bernardus C. J. Schimmel
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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12
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Nouhaud P, Gautier M, Gouin A, Jaquiéry J, Peccoud J, Legeai F, Mieuzet L, Smadja CM, Lemaitre C, Vitalis R, Simon JC. Identifying genomic hotspots of differentiation and candidate genes involved in the adaptive divergence of pea aphid host races. Mol Ecol 2018; 27:3287-3300. [PMID: 30010213 DOI: 10.1111/mec.14799] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Identifying the genomic bases of adaptation to novel environments is a long-term objective in evolutionary biology. Because genetic differentiation is expected to increase between locally adapted populations at the genes targeted by selection, scanning the genome for elevated levels of differentiation is a first step towards deciphering the genomic architecture underlying adaptive divergence. The pea aphid Acyrthosiphon pisum is a model of choice to address this question, as it forms a large complex of plant-specialized races and cryptic species, resulting from recent adaptive radiation. Here, we characterized genomewide polymorphisms in three pea aphid races specialized on alfalfa, clover and pea crops, respectively, which we sequenced in pools (poolseq). Using a model-based approach that explicitly accounts for selection, we identified 392 genomic hotspots of differentiation spanning 47.3 Mb and 2,484 genes (respectively, 9.12% of the genome size and 8.10% of its genes). Most of these highly differentiated regions were located on the autosomes, and overall differentiation was weaker on the X chromosome. Within these hotspots, high levels of absolute divergence between races suggest that these regions experienced less gene flow than the rest of the genome, most likely by contributing to reproductive isolation. Moreover, population-specific analyses showed evidence of selection in every host race, depending on the hotspot considered. These hotspots were significantly enriched for candidate gene categories that control host-plant selection and use. These genes encode 48 salivary proteins, 14 gustatory receptors, 10 odorant receptors, five P450 cytochromes and one chemosensory protein, which represent promising candidates for the genetic basis of host-plant specialization and ecological isolation in the pea aphid complex. Altogether, our findings open new research directions towards functional studies, for validating the role of these genes on adaptive phenotypes.
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Affiliation(s)
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
| | - Anaïs Gouin
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Fabrice Legeai
- INRA, UMR 1349 IGEPP, Le Rheu, France
- Inria/IRISA GenScale, Rennes, France
| | | | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554) - CNRS - IRD - EPHE - CIRAD -Université de Montpellier, Montpellier, France
| | | | - Renaud Vitalis
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- Institut de Biologie Computationnelle, Univ Montpellier, Montpellier, France
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13
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Brand P, Ramírez SR. The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees. Genome Biol Evol 2018; 9:2023-2036. [PMID: 28854688 PMCID: PMC5597890 DOI: 10.1093/gbe/evx149] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2017] [Indexed: 12/24/2022] Open
Abstract
Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects.
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Affiliation(s)
- Philipp Brand
- Department for Evolution and Ecology, Center for Population Biology, University of California, Davis.,Population Biology Graduate Group, Center for Population Biology, University of California, Davis
| | - Santiago R Ramírez
- Department for Evolution and Ecology, Center for Population Biology, University of California, Davis
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14
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Simon JC, Peccoud J. Rapid evolution of aphid pests in agricultural environments. CURRENT OPINION IN INSECT SCIENCE 2018; 26:17-24. [PMID: 29764656 DOI: 10.1016/j.cois.2017.12.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/30/2017] [Indexed: 05/19/2023]
Abstract
Aphids constitute a major group of crop pests that inflict serious damages to plants, both directly by ingesting phloem and indirectly as vectors of numerous diseases. In response to intense and repeated human-induced pressures, such as insecticide treatments, the use of resistant plants and biological agents, aphids have developed a series of evolutionary responses relying on adaptation and phenotypic plasticity. In this review, we highlight some remarkable evolutionary responses to anthropogenic pressures in agroecosystems and discuss the mechanisms underlying the ecological and evolutionary success of aphids. We outline the peculiar mode of reproduction, the polyphenism for biologically important traits and the diverse and flexible associations with microbial symbionts as key determinants of adaptive potential and pest status of aphids.
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Affiliation(s)
- Jean-Christophe Simon
- INRA, Institute of Genetics, Environment and Plant Protection (IGEPP-Joint Research Unit 1349), Domaine de la Motte, BP 35327, 35653 Le Rheu, France.
| | - Jean Peccoud
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions (EBI-Joint Research Unit 7267, CNRS), 86000 Poitiers, France
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15
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16
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Kulmuni J, Westram AM. Intrinsic incompatibilities evolving as a by-product of divergent ecological selection: Considering them in empirical studies on divergence with gene flow. Mol Ecol 2017; 26:3093-3103. [PMID: 28423210 DOI: 10.1111/mec.14147] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 12/31/2022]
Abstract
The possibility of intrinsic barriers to gene flow is often neglected in empirical research on local adaptation and speciation with gene flow, for example when interpreting patterns observed in genome scans. However, we draw attention to the fact that, even with gene flow, divergent ecological selection may generate intrinsic barriers involving both ecologically selected and other interacting loci. Mechanistically, the link between the two types of barriers may be generated by genes that have multiple functions (i.e., pleiotropy), and/or by gene interaction networks. Because most genes function in complex networks, and their evolution is not independent of other genes, changes evolving in response to ecological selection can generate intrinsic barriers as a by-product. A crucial question is to what extent such by-product barriers contribute to divergence and speciation-that is whether they stably reduce gene flow. We discuss under which conditions by-product barriers may increase isolation. However, we also highlight that, depending on the conditions (e.g., the amount of gene flow and the strength of selection acting on the intrinsic vs. the ecological barrier component), the intrinsic incompatibility may actually destabilize barriers to gene flow. In practice, intrinsic barriers generated as a by-product of divergent ecological selection may generate peaks in genome scans that cannot easily be interpreted. We argue that empirical studies on divergence with gene flow should consider the possibility of both ecological and intrinsic barriers. Future progress will likely come from work combining population genomic studies, experiments quantifying fitness and molecular studies on protein function and interactions.
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Affiliation(s)
- J Kulmuni
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - A M Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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17
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Comeault AA, Serrato-Capuchina A, Turissini DA, McLaughlin PJ, David JR, Matute DR. A nonrandom subset of olfactory genes is associated with host preference in the fruit fly Drosophila orena. Evol Lett 2017; 1:73-85. [PMID: 30283640 PMCID: PMC6121841 DOI: 10.1002/evl3.7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/27/2017] [Indexed: 12/18/2022] Open
Abstract
Specialization onto different host plants has been hypothesized to be a major driver of diversification in insects, and traits controlling olfaction have been shown to play a fundamental role in host preferences. A diverse set of olfactory genes control olfactory traits in insects, and it remains unclear whether specialization onto different hosts is likely to involve a nonrandom subset of these genes. Here, we test the role of olfactory genes in a novel case of specialization in Drosophila orena. We report the first population‐level sample of D. orena on the West African island of Bioko, since its initial collection in Cameroon in 1975, and use field experiments and behavioral assays to show that D. orena has evolved a strong preference for waterberry (Syzygium staudtii). We then show that a nonrandom subset of genes controlling olfaction‐–those controlling odorant‐binding and chemosensory proteins–‐have an enriched signature of positive selection relative to the rest of the D. orena genome. By comparing signatures of positive selection on olfactory genes between D. orena and its sister species, D. erecta we show that odorant‐binding and chemosensory have evidence of positive selection in both species; however, overlap in the specific genes with evidence of selection in these two classes is not greater than expected by chance. Finally, we use quantitative complementation tests to confirm a role for seven olfactory loci in D. orena’s preference for waterberry fruit. Together, our results suggest that D. orena and D. erecta have specialized onto different host plants through convergent evolution at the level of olfactory gene family, but not at specific olfactory genes.
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Affiliation(s)
- Aaron A Comeault
- Department of Biology University of North Carolina Chapel Hill North Carolina 27599
| | | | - David A Turissini
- Department of Biology University of North Carolina Chapel Hill North Carolina 27599
| | - Patrick J McLaughlin
- Department of Biology Drexel University Philadelphia Pennsylvania 19104.,Bioko Biodiversity Protection Program Bioko Island Equatorial Guinea
| | - Jean R David
- Laboratoire Evolution, Genomes, Speciation (LEGS) CNRS Gif sur Yvette Cedex France.,Université Paris-Sud Orsay Cedex France.,Département Systématique et Evolution Museum National d'Histoire Naturelle (MNHN) UMR 7205 (OSEB) Paris France
| | - Daniel R Matute
- Department of Biology University of North Carolina Chapel Hill North Carolina 27599
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18
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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19
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Rogers SM, Xu S, Schlüter PM. Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation. Mol Ecol 2017; 26:1-6. [DOI: 10.1111/mec.13947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/30/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Sean M. Rogers
- Department of Biological Sciences; University of Calgary; Calgary Alberta Canada T3L 2R9
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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20
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Byers KJRP, Xu S, Schlüter PM. Molecular mechanisms of adaptation and speciation: why do we need an integrative approach? Mol Ecol 2016; 26:277-290. [DOI: 10.1111/mec.13678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Kelsey J. R. P. Byers
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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