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Choi TY, Lee SR. Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes. PLoS One 2024; 19:e0301346. [PMID: 38578735 PMCID: PMC10997070 DOI: 10.1371/journal.pone.0301346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, Chosun University, Gwangju, South Korea
| | - Soo-Rang Lee
- Department of Biology Education, Chosun University, Gwangju, South Korea
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Bouvier JW, Kelly S. Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154021. [PMID: 37392528 DOI: 10.1016/j.jplph.2023.154021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Rubisco is the primary entry point for carbon into the biosphere. It has been widely proposed that rubisco is highly constrained by catalytic trade-offs due to correlations between the enzyme's kinetic traits across species. In previous work, we have shown that the strength of these correlations, and thus the strength of catalytic trade-offs, have been overestimated due to the presence of phylogenetic signal in the kinetic trait data (Bouvier et al., 2021). We demonstrated that only the trade-offs between the Michaelis constant for CO2 and carboxylase turnover, and between the Michaelis constants for CO2 and O2 were robust to phylogenetic effects. We further demonstrated that phylogenetic constraints have limited rubisco adaptation to a greater extent than the combined action of catalytic trade-offs. Recently, however, our claims have been contested by Tcherkez and Farquhar (2021), who have argued that the phylogenetic signal we detect in rubisco kinetic traits is an artefact of species sampling, the use of rbcL-based trees for phylogenetic inference, laboratory-to-laboratory variability in kinetic measurements, and homoplasy of the C4 trait. In the present article, we respond to these criticisms on a point-by-point basis and conclusively show that all are unfounded. As such, we stand by our original conclusions. Namely, although rubisco kinetic evolution has been limited by biochemical trade-offs, these are not absolute and have been previously overestimated due to phylogenetic biases. Instead, rubisco adaptation has in fact been more limited by phylogenetic constraint.
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Affiliation(s)
- Jacques W Bouvier
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
| | - Steven Kelly
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.
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Xia Q, Zhang H, Lv D, El-Kassaby YA, Li W. Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes. BMC Genomics 2023; 24:346. [PMID: 37349702 DOI: 10.1186/s12864-023-09439-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species. RESULTS Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification. CONCLUSION We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
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Affiliation(s)
- Qijing Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongbin Zhang
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Dong Lv
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Joyce EM, Appelhans MS, Buerki S, Cheek M, de Vos JM, Pirani JR, Zuntini AR, Bachelier JB, Bayly MJ, Callmander MW, Devecchi MF, Pell SK, Groppo M, Lowry PP, Mitchell J, Siniscalchi CM, Munzinger J, Orel HK, Pannell CM, Nauheimer L, Sauquet H, Weeks A, Muellner-Riehl AN, Leitch IJ, Maurin O, Forest F, Nargar K, Thiele KR, Baker WJ, Crayn DM. Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication. FRONTIERS IN PLANT SCIENCE 2023; 14:1063174. [PMID: 36959945 PMCID: PMC10028101 DOI: 10.3389/fpls.2023.1063174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.
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Affiliation(s)
- Elizabeth M. Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Munich, Germany
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Marc S. Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Goettingen, Germany
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, United States
| | - Martin Cheek
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jurriaan M. de Vos
- Department of Environmental Sciences, University Basel, Basel, Switzerland
| | - José R. Pirani
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | | | | | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marcelo F. Devecchi
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Susan K. Pell
- United States Botanic Garden, Washington, DC, United States
| | - Milton Groppo
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, United States
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - John Mitchell
- New York Botanical Garden, New York, NY, United States
| | - Carolina M. Siniscalchi
- Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS, United States
| | - Jérôme Munzinger
- AMAP, Université Montpellier, Institut de Recherche pour le Développement (IRD), Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Centre National de la Recherche Scientifique (CNRS), Institut national de la recherche agronomique (INRAE), Montpellier, France
| | - Harvey K. Orel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Caroline M. Pannell
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Biology, Oxford University, Oxford, United Kingdom
- Marine Laboratory, Queen’s University Belfast, Portaferry, United Kingdom
| | - Lars Nauheimer
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Andrea Weeks
- Department of Biology, George Mason University, Fairfax, VA, United States
| | - Alexandra N. Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organization (CSIRO), Canberra, ACT, Australia
| | - Kevin R. Thiele
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | | | - Darren M. Crayn
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
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Han S, Ding H, Bi D, Zhang S, Yi R, Gao J, Yang J, Ye Y, Wu L, Kan X. Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales. PLANTS (BASEL, SWITZERLAND) 2022; 11:3544. [PMID: 36559654 PMCID: PMC9787361 DOI: 10.3390/plants11243544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinming Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Dubois B, Debode F, Hautier L, Hulin J, Martin GS, Delvaux A, Janssen E, Mingeot D. A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data. BMC Genom Data 2022; 23:53. [PMID: 35804326 PMCID: PMC9264521 DOI: 10.1186/s12863-022-01067-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence. Results We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets. Conclusion This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01067-5.
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Montenegro JD, Julca I, Chumbe-Nolasco LD, Rodríguez-Pérez LM, Sevilla Panizo R, Medina-Hoyos A, Gutiérrez-Reynoso DL, Guerrero-Abad JC, Amasifuen Guerra CA, García-Serquén AL. Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. 'INIA 601'. PLANTS (BASEL, SWITZERLAND) 2022; 11:2727. [PMID: 36297753 PMCID: PMC9612013 DOI: 10.3390/plants11202727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace 'Kculli', but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar 'INIA 601' with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America.
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Affiliation(s)
- Juan D. Montenegro
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- Department of Neurosciences and Developmental Biology, University of Vienna, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Irene Julca
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Lenin D. Chumbe-Nolasco
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Lila M. Rodríguez-Pérez
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Ricardo Sevilla Panizo
- Departamento de Fitotecnia, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, Peru
| | - Alicia Medina-Hoyos
- Estación Experimental Agraria “Baños del Inca”, Instituto Nacional de Innovación Agraria (INIA), Km. 5.5 Carretera Cajamarca–Celendín, Cajamarca 06000, Peru
| | - Dina L. Gutiérrez-Reynoso
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Juan Carlos Guerrero-Abad
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos A. Amasifuen Guerra
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Aura L. García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
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8
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Simmons MP, Maurin O, Bailey P, Brewer GE, Roy S, Lombardi JA, Forest F, Baker WJ. Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales. Cladistics 2022; 38:595-611. [PMID: 35569142 DOI: 10.1111/cla.12507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2022] [Indexed: 01/31/2023] Open
Abstract
We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523-1878, USA
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Julio A Lombardi
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista - UNESP, Av. 24-A 1515 - Bela Vista, Caixa Postal 199, São Paulo, Brazil
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Elshikh MS, Ajmal Ali M, Al-Hemaid F, Yong Kim S, Elangbam M, Bahadur Gurung A, Mukherjee P, El-Zaidy M, Lee J. Insights into plastome of Fagonia indica Burm.f. (Zygophyllaceae) : organization, annotation and phylogeny. Saudi J Biol Sci 2022; 29:1313-1321. [PMID: 35280582 PMCID: PMC8913386 DOI: 10.1016/j.sjbs.2021.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/15/2022] Open
Abstract
The enhanced understanding of chloroplast genomics would facilitate various biotechnology applications; however, the chloroplast (cp) genome / plastome characteristics of plants like Fagonia indica Burm.f. (family Zygophyllaceae), which have the capability to grow in extremely hot sand desert, have been rarely understood. The de novo genome sequence of F. indica using the Illumina high-throughput sequencing technology determined 128,379 bp long cp genome, encode 115 unique coding genes. The present study added the evidence of the loss of a copy of the IR in the cp genome of the taxa capable to grow in the hot sand desert. The maximum likelihood analysis revealed two distinct sub-clades i.e. Krameriaceae and Zygophyllaceae of the order Zygophyllales, nested within fabids.
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Affiliation(s)
- Mohamed S Elshikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad Al-Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Soo Yong Kim
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Meena Elangbam
- Genetics Laboratory, Centre of Advanced Studies in Life Sciences, Manipur University, Canchipur 795 003, India
| | - Arun Bahadur Gurung
- Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong-793022, Meghalaya, India
| | - Prasanjit Mukherjee
- Department of Botany, Kumar Kalidas Memorial College, Pakur-816107, Jharkhand, India
| | - Mohamed El-Zaidy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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10
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Asaf S, Ahmad W, Al-Harrasi A, Khan AL. Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae). BMC Genomics 2022; 23:83. [PMID: 35086490 PMCID: PMC8796432 DOI: 10.1186/s12864-022-08320-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species. RESULTS The results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae. CONCLUSION All the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman
| | - Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Houston, TX, 77479, USA.
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11
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Omar HS, Al Mutery A, Osman NH, Reyad NEHA, Abou-Zeid MA. Genetic diversity, antifungal evaluation and molecular docking studies of Cu-chitosan nanoparticles as prospective stem rust inhibitor candidates among some Egyptian wheat genotypes. PLoS One 2021; 16:e0257959. [PMID: 34767570 PMCID: PMC8589204 DOI: 10.1371/journal.pone.0257959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/14/2021] [Indexed: 11/21/2022] Open
Abstract
Wheat has a remarkable importance among cereals worldwide. Wheat stem and leaf rust constitute the main threats that destructively influence grain quality and yield production. Pursuing resistant cultivars and developing new genotypes including resistance genes is believed to be the most effective tool to overcome these challenges. This study is the first to use molecular markers to evaluate the genetic diversity of eighteen Egyptian wheat genotypes. Moreover, the molecular docking analysis was also used to assess the Cu-chitosan nanoparticle (CuChNp) treatment and its mode of action in disease control management. The tested genotypes were categorized into two main cluster groups depending on the similarity matrix, i.e the most resistant and susceptible genotypes to stem and leaf rust races. The results of SCoT primers revealed 140 polymorphic and 5 monomorphic bands with 97% polymorphism. While 121 polymorphic and 74 monomorphic bands were scored for SRAP primers (99% polymorphism). The genotypes Sakha 94, Sakha 95, Beni Sweif 4, Beni Sweif 7, Sohag 4 and Sohag 5 were resistant, while Giza 160 was highly susceptible to all stem rust races at the seedling stage. However, in the adult stage, the 18 genotypes were evaluated for stem and leaf rust-resistant in two different locations, i.e. Giza and Sids. In this investigation, for the first time, the activity of CuChNp was studied and shown to have the potential to inhibit stem and leaf rust in studied Egyptian wheat genotypes. The Spraying Cu-chitosan nanoparticles showed that the incubation and latent periods were increased in treated plants of the tested genotypes. Molecular modeling revealed their activity against the stem and leaf rust development. The SRAP and SCoT markers were highly useful tools for the classification of the tested wheat genotypes, although they displayed high similarities at the morphological stage. However, Cu-chitosan nanoparticles have a critical and effective role in stem and leaf rust disease control.
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Affiliation(s)
- Hanaa S. Omar
- Faculty of Agriculture, Genetics Department, Cairo University, Giza, Egypt
- GMO lab Faculty of Agriculture, Cairo University, Research Park, CURP, Giza, Egypt
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Molecular Genetics and Stem Cell Research Laboratory, University of Sharjah, Sharjah, United Arab Emirates
| | - Neama H. Osman
- Faculty of Agriculture, Genetics Department, Cairo University, Giza, Egypt
| | | | - Mohamed A. Abou-Zeid
- Wheat Disease Research Department, Plant Pathology Research Institute, ARC, Giza, Egypt
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12
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Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, Cai J, Gitzendanner MA, Fritsch PW, Zhang T, Jin JJ, Zeng CX, Wang H, Yu WB, Zhang R, van der Bank M, Olmstead RG, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Yi TS, Li DZ. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 2021; 19:232. [PMID: 34711223 PMCID: PMC8555322 DOI: 10.1186/s12915-021-01166-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. RESULTS Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. CONCLUSIONS We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lu Gan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hong Wang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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13
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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14
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Tian YM, Huang J, Su T, Zhang ST. Early Oligocene Itea (Iteaceae) leaves from East Asia and their biogeographic implications. PLANT DIVERSITY 2021; 43:142-151. [PMID: 33997547 PMCID: PMC8103422 DOI: 10.1016/j.pld.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 06/12/2023]
Abstract
Compressed materials of fossil foliage described here as Itea polyneura sp. nov. (Iteaceae) were collected from the Oligocene of Wenshan, Yunnan Province, southwestern China. The identification is based on the following characters: eucamptodromous secondary veins, strict scalariform tertiary veins, irregular tooth with setaceous apex. The leaf morphology of all modern and fossil species was compared with the new species from Wenshan and show that I. polyneura is most similar to the extant East Asian species Itea omeiensis, which inhabits subtropical forests of southern China. This discovery represents the first unambiguous leaf fossil record of Itea in East Asia. Together with other species in the Wenshan flora and evidence from several other flora in southern China, these findings demonstrate that Itea from East Asia arose with the Paleogene modernization.
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Affiliation(s)
- Yi-Min Tian
- Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jian Huang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Tao Su
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shi-Tao Zhang
- Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
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15
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Ali MA. Phylotranscriptomic analysis of Dillenia indica L. (Dilleniales, Dilleniaceae) and its systematics implication. Saudi J Biol Sci 2021; 28:1557-1560. [PMID: 33732040 PMCID: PMC7938110 DOI: 10.1016/j.sjbs.2021.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
The recent massive development in the next-generation sequencing platforms and bioinformatics tools including cloud based computing have proven extremely useful in understanding the deeper-level phylogenetic relationships of angiosperms. The present phylotranscriptomic analyses address the poorly known evolutionary relationships of the order Dilleniales to order of the other angiosperms using the minimum evolution method. The analyses revealed the nesting of the representative taxon of Dilleniales in the MPT but distinct from the representative of the order Santalales, Caryophyllales, Asterales, Cornales, Ericales, Lamiales, Saxifragales, Fabales, Malvales, Vitales and Berberidopsidales.
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Affiliation(s)
- Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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16
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Cabral FN, Trad RJ, Amorim BS, Maciel JR, Amaral MDCED, Stevens P. Phylogeny, divergence times, and diversification in Calophyllaceae: Linking key characters and habitat changes to the evolution of Neotropical Calophylleae. Mol Phylogenet Evol 2021; 157:107041. [PMID: 33476719 DOI: 10.1016/j.ympev.2020.107041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/11/2020] [Accepted: 12/08/2020] [Indexed: 11/30/2022]
Abstract
The clusioid clade comprises five monophyletic families: Bonnetiaceae, Calophyllaceae, Clusiaceae s.s., Hypericaceae, and Podostemaceae. Even though the circumscription of these families is well established, phylogenetic relationships within some families remain unresolved. This study aims to infer phylogenetic relationships within the Neotropical Calophylleae based on a broad sampling of taxa and a multilocus approach. We then use our phylogenetic framework as basis to investigate the evolution and biogeography of Calophylleae and diversification shifts in Calophyllaceae. To reconstruct the phylogeny of the Neotropical Calophylleae, we used five plastid (matK, ndhF, rbcL, psbA-trnH, and trnK), two mitochondrial (matR and rps3), and two nuclear (EMB2765 and ITS) markers, including previously published and newly generated sequences. We sampled 74 species, increasing sampling of Neotropical taxa by 500%. Our phylogenetic hypothesis for Calophyllaceae provides additional support for the monophyly of all genera and allowed us to identify four main clades: Calophyllum, Kayea, Mammea, and the Neotropical clade. The Neotropical clade includes three main lineages, a small clade composed of Clusiella and Marila, and a large HaCaKi clade (i.e., Haplocarpa, Caraipa, and Kilmeyera) that is sister to Mahurea exstipulata. The evolution of three morphological traits (i.e., fleshy fruits, anther glands, and winged seeds) were shown to be associated with changes in evolutionary dynamics in Calophyllaceae, while a biome shift was detected in Kielmeyera, affecting net diversification within this genus. Major geological and climatic events such as the Andean uplift and a gradual decrease in temperatures seem to have influenced diversification rates within the Neotropical Calophylleae.
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Affiliation(s)
- Fernanda Nunes Cabral
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, 13083-862 Campinas, SP, Brazil; Departamento de Ciências e Linguagens, Instituto Federal de Minas Gerais - Campus Bambuí, 38900-000 Bambuí, MG, Brazil.
| | - Rafaela Jorge Trad
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, 13083-862 Campinas, SP, Brazil
| | - Bruno Sampaio Amorim
- Museu da Amazônia, MUSA, 69099-415 Manaus, AM, Brazil; Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia (PPGMBT-UEA), Universidade do Estado do Amazonas, 69065-001 Manaus, AM, Brazil
| | | | - Maria do Carmo Estanislau do Amaral
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, 13083-862 Campinas, SP, Brazil
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17
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Zhang C, Huelsenbeck JP, Ronquist F. Using Parsimony-Guided Tree Proposals to Accelerate Convergence in Bayesian Phylogenetic Inference. Syst Biol 2020; 69:1016-1032. [PMID: 31985810 PMCID: PMC7440752 DOI: 10.1093/sysbio/syaa002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as "convergence") and in estimating the correct proportions of the different types of them (known as "mixing"). Here, we introduce a new class of moves, which propose trees based on their parsimony scores. The proposal distribution derived from the parsimony scores is a quickly computable albeit rough approximation of the conditional posterior distribution over candidate trees. We demonstrate with simulations that parsimony-guided moves correctly sample the uniform distribution of topologies from the prior. We then evaluate their performance against standard moves using six challenging empirical data sets, for which we were able to obtain accurate reference estimates of the posterior using long MCMC runs, a mix of topology proposals, and Metropolis coupling. On these data sets, ranging in size from 357 to 934 taxa and from 1740 to 5681 sites, we find that single chains using parsimony-guided moves usually converge an order of magnitude faster than chains using standard moves. They also exhibit better mixing, that is, they cover the most probable trees more quickly. Our results show that tree moves based on quick and dirty estimates of the posterior probability can significantly outperform standard moves. Future research will have to show to what extent the performance of such moves can be improved further by finding better ways of approximating the posterior probability, taking the trade-off between accuracy and speed into account. [Bayesian phylogenetic inference; MCMC; parsimony; tree proposal.].
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Affiliation(s)
- Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 XizhimenWai Street, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 142 XizhimenWai Street, Beijing 100044, China
| | - John P Huelsenbeck
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden
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Gernandt DS, Platt JL, Stone JK, Spatafor JW, Holst-Jensen A, Hamelin RC, Kohn LM. Phylogenetics of Helotiales and Rhytismatales based on partial small subunit nuclear ribosomal DNA sequences. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- David S. Gernandt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Jamie L. Platt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Jeffrey K. Stone
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Joseph W. Spatafor
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Arne Holst-Jensen
- National Veterinary Institute, Section of Food & Feed Microbiology, Ullevålsveien 68, P.O. Box 8156 Dep. 0033 Oslo, Norway
| | - Richard C. Hamelin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, P.O. Box 3800, 1055 rue du P.E.P.S., Sainte-Foy, QC G1V 4C7 Canada
| | - Linda M. Kohn
- Department of Botany, University of Toronto, Erindale Campus, Mississauga, Ontario L5L 1C6 Canada
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19
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Gomes Pacheco T, de Santana Lopes A, Monteiro Viana GD, Nascimento da Silva O, Morais da Silva G, do Nascimento Vieira L, Guerra MP, Nodari RO, Maltempi de Souza E, de Oliveira Pedrosa F, Otoni WC, Rogalski M. Genetic, evolutionary and phylogenetic aspects of the plastome of annatto (Bixa orellana L.), the Amazonian commercial species of natural dyes. PLANTA 2019; 249:563-582. [PMID: 30310983 DOI: 10.1007/s00425-018-3023-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
The plastome of B. orellana reveals specific evolutionary features, unique RNA editing sites, molecular markers and the position of Bixaceae within Malvales. Annatto (Bixa orellana L.) is a native species of tropical Americas with center of origin in Brazilian Amazonia. Its seeds accumulate the apocarotenoids, bixin and norbixin, which are only found in high content in this species. The seeds of B. orellana are commercially valued by the food industry because its dyes replace synthetic ones from the market due to potential carcinogenic risks. The increasing consumption of B. orellana seeds for dye extraction makes necessary the increase of productivity, which is possible accessing the genetic basis and searching for elite genotypes. The identification and characterization of molecular markers are essential to analyse the genetic diversity of natural populations and to establish suitable strategies for conservation, domestication, germplasm characterization and genetic breeding. Therefore, we sequenced and characterized in detail the plastome of B. orellana. The plastome of B. orellana is a circular DNA molecule of 159,708 bp with a typical quadripartite structure and 112 unique genes. Additionally, a total of 312 SSR loci were identified in the plastome of B. orellana. Moreover, we predicted in 23 genes a total of 57 RNA-editing sites of which 11 are unique for B. orellana. Furthermore, our plastid phylogenomic analyses, using the plastome sequences available in the plastid database belonging to species of order Malvales, indicate a closed relationship between Bixaceae and Malvaceae, which formed a sister group to Thymelaeaceae. Finally, our study provided useful data to be employed in several genetic and biotechnological approaches in B. orellana and related species of the family Bixaceae.
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Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gélia Dinah Monteiro Viana
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia Vegetal, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Chen ZS, Hou DH, Cheng XW, Wang X, Huang GH. Genomic analysis of a novel isolate Heliothis virescens ascovirus 3i (HvAV-3i) and identification of ascoviral repeat ORFs (aros). Arch Virol 2018; 163:2849-2853. [PMID: 29948385 DOI: 10.1007/s00705-018-3899-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 01/08/2023]
Abstract
Ascoviruses are circular double-stranded DNA viruses that infect insects. Herein we sequenced and analyzed the genome of the previously unrecorded ascovirus isolate Heliothis virescens ascovirus 3i (HvAV-3i). The genome size is 185,650 bp with 181 hypothetical open reading frames (ORFs). Additionally, definition based on ascovirus repeated ORFs (aros) is proposed; whereby the 29 aros from all sequenced Ascoviridae genomes are divided into six distinct groups. The topological relationship among the isolates of Heliothis virescens ascovirus 3a is (HvAV-3f, {HvAV-3h, [HvAV-3e, (HvAV-3g, HvAV-3i)]}) with every clade well supported by a Bayesian posterior probability of 1.00 and a Bootstrap value of 100%.
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Affiliation(s)
- Zi-Shu Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, Hunan, China
- Institute of Virology, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Dian-Hai Hou
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xiao-Wen Cheng
- Department of Microbiology, 56 Pearson Hall, Miami University, Oxford, 45056, Ohio, USA
| | - Xing Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, Hunan, China
- Institute of Virology, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Guo-Hua Huang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, Hunan, China.
- Institute of Virology, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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Godoy-Bürki AC, Acosta JM, Aagesen L. Phylogenetic relationships within the New World subfamily Larreoideae (Zygophyllaceae) confirm polyphyly of the disjunct genus Bulnesia. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1451406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- A. C. Godoy-Bürki
- Instituto de Botánica Darwinion, Labardén 200, Casilla de correo 22, B1642HYD San Isidro, Buenos Aires, Argentina
| | - J. M. Acosta
- Instituto de Botánica Darwinion, Labardén 200, Casilla de correo 22, B1642HYD San Isidro, Buenos Aires, Argentina
| | - L. Aagesen
- Instituto de Botánica Darwinion, Labardén 200, Casilla de correo 22, B1642HYD San Isidro, Buenos Aires, Argentina
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Stull GW, Schori M, Soltis DE, Soltis PS. Character evolution and missing (morphological) data across Asteridae. AMERICAN JOURNAL OF BOTANY 2018; 105:470-479. [PMID: 29656519 DOI: 10.1002/ajb2.1050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/08/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Our current understanding of flowering plant phylogeny provides an excellent framework for exploring various aspects of character evolution through comparative analyses. However, attempts to synthesize this phylogenetic framework with extensive morphological data sets have been surprisingly rare. Here, we explore character evolution in Asteridae (asterids), a major angiosperm clade, using an extensive morphological data set and a well-resolved phylogeny. METHODS We scored 15 phenotypic characters (spanning chemistry, vegetative anatomy, and floral, fruit, and seed features) across 248 species for ancestral state reconstruction using a phylogenetic framework based on 73 plastid genes and the same 248 species. KEY RESULTS Iridoid production, unitegmic ovules, and cellular endosperm were all reconstructed as synapomorphic for Asteridae. Sympetaly, long associated with asterids, shows complex patterns of evolution, suggesting it arose several times independently within the clade. Stamens equal in number to the petals is likely a synapomorphy for Gentianidae, a major asterid subclade. Members of Lamianae, a major gentianid subclade, are potentially diagnosed by adnate stamens, unilacunar nodes, and simple perforation plates. CONCLUSIONS The analyses presented here provide a greatly improved understanding of character evolution across Asteridae, highlighting multiple characters potentially synapomorphic for major clades. However, several important parts of the asterid tree are poorly known for several key phenotypic features (e.g., degree of petal fusion, integument number, nucellus type, endosperm type, iridoid production). Further morphological, anatomical, developmental, and chemical investigations of these poorly known asterids are critical for a more detailed understanding of early asterid evolution.
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Affiliation(s)
- Gregory W Stull
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Melanie Schori
- United States Department of Agriculture, National Germplasm Resources Laboratory, Beltsville, MD, 20705-2305, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611-7800, USA
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Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales. Mol Phylogenet Evol 2018; 121:198-211. [PMID: 29360618 DOI: 10.1016/j.ympev.2018.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 01/05/2023]
Abstract
Relationships among the genera of the small, woody family Styracaceae and among families of the large, diverse order Ericales have resisted complete resolution with sequences from one or a few genes. We used plastome sequencing to attempt to resolve the backbone relationships of Styracaceae and Ericales and to explore plastome structural evolution. Complete plastomes for 23 species are newly reported here, including 18 taxa of Styracaceae and five of Ericales (including species of Sapotaceae, Clethraceae, Symplocaceae, and Diapensiaceae). Combined with publicly available complete plastome data, this resulted in a data set of 60 plastomes, including 11 of the 12 genera of Styracaceae and 12 of 22 families of Ericales. Styracaceae plastomes were found to possess the quadripartite structure typical of angiosperms, with sizes ranging from 155 to 159 kb. Most of the plastomes were found to possess the full complement of typical angiosperm plastome genes. Unusual structural features were detected in plastomes of Alniphyllum and Bruinsmia, including the presence of a large 20-kb inversion (14 genes) in the Large Single-Copy region, the loss or pseudogenization of the clpP and accD genes in Bruinsmia, and the loss of the first exon of rps16 in B. styracoides. Likewise, the second intron from clpP was found to be lost in Alniphyllum and Huodendron. Phylogenomic analyses including all 79 plastid protein-coding genes provided improved resolution for relationships among the genera of Styracaceae and families of Ericales. Styracaceae was strongly supported as monophyletic, with Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia successively sister to the remainder of the family, all with strong support. All genera of Styracaceae were recovered as monophyletic, except for Halesia and Pterostyrax, which were each recovered as polyphyletic with strong support. Within Ericales, all families were recovered as monophyletic with strong support, with Balsaminaceae sister to remaining Ericales. Most relationships recovered in plastome analyses are congruent with previous analyses based on smaller data sets. Our results demonstrate the power of plastid phylogenomics to improve phylogenetic hypotheses among genera and families, and provide new insight into plastome evolution across Ericales.
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Ruiz C, Nadal A, Foix L, Montesinos L, Montesinos E, Pla M. Diversity of plant defense elicitor peptides within the Rosaceae. BMC Genet 2018; 19:11. [PMID: 29361905 PMCID: PMC5782389 DOI: 10.1186/s12863-017-0593-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant elicitor peptides (Peps) are endogenous molecules that induce and amplify the first line of inducible plant defense, known as pattern-triggered immunity, contributing to protect plants against attack by bacteria, fungi and herbivores. Pep topic application and transgenic expression have been found to enhance disease resistance in a small number of model plant-pathogen systems. The action of Peps relies on perception by specific receptors, so displaying a family-specific activity. Recently, the presence and activity of Peps within the Rosaceae has been demonstrated. Here we characterized the population of Pep sequences within the economically important plant family of Rosaceae, with special emphasis on the Amygdaleae and Pyreae tribes, which include the most relevant edible species such as apple, pear and peach, and numerous ornamental and wild species (e.g. photinia, firethorn and hawthorn). RESULTS The systematic experimental search for Pep and the corresponding precursor PROPEP sequences within 36 Amygdaleae and Pyreae species, and 100 cultivars had a highly homogeneous pattern, with two tribe-specific Pep types per plant, i.e. Pep1 and Pep2 (Amygdaleae) or Pep3 and Pep4 (Pyreae). Pep2 and Pep3 are highly conserved, reaching identity percentages similar to those of genes used in plant phylogenetic analyses, while Pep1 and Pep4 are somewhat more variable, with similar values to the corresponding PROPEPs. In contrast to Pep3 and Pep4, Pep1 and Pep2 sequences of different species paralleled their phylogenetic relationships, and putative ancestor sequences were identified. The large amount of sequences allowed refining of a C-terminal consensus sequence that would support the protective activity of Pep1-4 in a Prunus spp. and Xanthomonas arboricola pv. pruni system. Moreover, tribe-specific consensus sequences were deduced at the center and C-terminal regions of Peps, which might explain the higher protection efficiencies described upon topic treatments with Peps from the same tribe. CONCLUSIONS The present study substantially enhances the knowledge on Peps within the Amygdaleae and Pyreae species. It can be the basis to design and fine-tune new control tools against important plant pathogens affecting Prunus, Pyrus and Malus species.
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Affiliation(s)
- Cristina Ruiz
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Anna Nadal
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Laura Foix
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Laura Montesinos
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Emilio Montesinos
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Maria Pla
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain.
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Hyldgaard B, Lambertini C, Brix H. Phylogeography reveals a potential cryptic invasion in the Southern Hemisphere of Ceratophyllum demersum, New Zealand's worst invasive macrophyte. Sci Rep 2017; 7:16569. [PMID: 29185467 PMCID: PMC5707378 DOI: 10.1038/s41598-017-16712-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
Ceratophyllum demersum (common hornwort) is presently considered the worst invasive submerged aquatic macrophyte in New Zealand. We explored the global phylogeographic pattern of the species, based on chloroplast and nuclear DNA, in order to identify the origin of the invasive populations in New Zealand and to clarify if there were multiple introductions. The phylogeographic study identified geographically differentiated gene pools in North America, tropical Asia, Australia, and South Africa, likely native to these regions, and a recent dispersal event of a Eurasian-related haplotype to North America, New Zealand, Australia, and South Africa. At least two different invasive genotypes of this Eurasian-related haplotype have been found in New Zealand. One genotype is closely related to genotypes in Australia and South Africa, while we could not trace the closest relatives of the other genotype within our C. demersum sample set. Contrasting spectra of genetic distances in New Zealand and in a region within the native range (Denmark), suggest that the invasive population was founded by vegetative reproduction, seen as low genetic distances among genotypes. We also discovered the introduction of the same Eurasian-related haplotype in Australia and South Africa and that a cryptic invasion may be occurring in these continents.
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Affiliation(s)
- Benita Hyldgaard
- Department of Bioscience, Section of Aquatic Biology, Aarhus University, Aarhus, Denmark.
- Department of Food Science, Section of Plants, Food and Climate, Aarhus University, Aarslev, Denmark.
| | - Carla Lambertini
- Department of Bioscience, Section of Aquatic Biology, Aarhus University, Aarhus, Denmark
| | - Hans Brix
- Department of Bioscience, Section of Aquatic Biology, Aarhus University, Aarhus, Denmark
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Thaowetsuwan P, Honorio Coronado EN, Ronse De Craene LP. Floral morphology and anatomy of Ophiocaryon, a paedomorphic genus of Sabiaceae. ANNALS OF BOTANY 2017; 120:819-832. [PMID: 29077782 PMCID: PMC5691798 DOI: 10.1093/aob/mcx115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/22/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS Ophiocaryon is a lesser known genus in Sabiaceae. This study examines flowers of six Ophiocaryon species in comparison with Meliosmaalba, to identify taxonomically informative characters for understanding relationships within the family Sabiaceae, to imply previously unknown pollination mechanisms of Ophiocaryon, and to contribute to the placement of Sabiaceae within the early-diverging eudicots. METHODS Floral morphology and anatomy of six Ophiocaryon species and M. alba were studied and described using scanning electron microscopy, clearing techniques and resin sectioning. KEY RESULTS Novel characters of Ophiocaryon were identified, e.g. conical cells on petals, different kinds of orbicules in anthers, stomata on nectary appendage tips and ovary, two distinct surface patterns on stamens and ovary, tanniferous cell layers in the ovary wall, and acorn-shaped unitegmic ovules with very short integuments. Comparison of floral characters between Ophiocaryon and Meliosma found that the calyx, corolla, androecium and gynoecium of Ophiocaryon resemble an undeveloped state of the latter taxon, reflecting a paedomorphic regression of the flower of Ophiocaryon. The flower morphology and anatomy of Ophiocaryon was compared with its putative sister species M. alba, but no clear shared derived characters could be detected. Moreover, the findings of scent, presence of conical cells on petals and a nectary suggest flowers are pollinated by small insects with a secondary pollen presentation on the cupula of fertile stamens. CONCLUSIONS We found that Ophiocaryon may be derived from ancestors that were similar to extant Meliosma in their flower structure and pollination mechanism. However, the lack of shared derived characters between Ophiocaryon and its phylogenetic sister group M. alba is puzzling and requires further investigations on the diversity of the latter species.
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Affiliation(s)
- P Thaowetsuwan
- Royal Botanic Garden Edinburgh (RBGE), Edinburgh, UK
- School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, The King’s Buildings, Edinburgh, UK
| | - E N Honorio Coronado
- Instituto de Investigaciones de la Amazonía Peruana (IIAP), Iquitos, Loreto, Peru
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Barta CE, Bolander B, Bilby SR, Brown JH, Brown RN, Duryee AM, Edelman DR, Gray CE, Gossett C, Haddock AG, Helsel MM, Jones AD, Klingseis ME, Leslie K, Miles EW, Prawitz RA. In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes. PLANTS (BASEL, SWITZERLAND) 2017; 6:E52. [PMID: 29073736 PMCID: PMC5750628 DOI: 10.3390/plants6040052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/29/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022]
Abstract
Mature oak (Quercus spp.) leaves, although abundantly available during the plants' developmental cycle, are rarely exploited as viable sources of genomic DNA. These leaves are rich in metabolites difficult to remove during standard DNA purification, interfering with downstream molecular genetics applications. The current work assessed whether in situ dark adaptation, to deplete sugar reserves and inhibit secondary metabolite synthesis could compensate for the difficulties encountered when isolating DNA from mature leaves rich in secondary metabolites. We optimized a rapid, commercial kit based method to extract genomic DNA from dark- and light-adapted leaves. We demonstrated that in situ dark adaptation increases the yield and quality of genomic DNA obtained from mature oak leaves, yielding templates of sufficiently high quality for direct downstream applications, such as PCR amplification and gene identification. The quality of templates isolated from dark-adapted pin oak leaves particularly improved the amplification of larger fragments in our experiments. From DNA extracts prepared with our optimized method, we identified for the first time partial segments of the genes encoding 18S rRNA and isoprene synthase (IspS) from pin oak (Quercus palustris), whose full genome has not yet been sequenced.
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Affiliation(s)
- Csengele E Barta
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Bethany Bolander
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Steven R Bilby
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Jeremy H Brown
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Reid N Brown
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Alexander M Duryee
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Danielle R Edelman
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Christina E Gray
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Chandler Gossett
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Amie G Haddock
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Mackenzie M Helsel
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Alyssa D Jones
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Marissa E Klingseis
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Kalif Leslie
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Edward W Miles
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Rachael A Prawitz
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
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Liao Y, De Grave S, Ho TW, Ip BH, Tsang LM, Chan TY, Chu KH. Molecular phylogeny of Pasiphaeidae (Crustacea, Decapoda, Caridea) reveals systematic incongruence of the current classification. Mol Phylogenet Evol 2017; 115:171-180. [DOI: 10.1016/j.ympev.2017.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
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Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0214-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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30
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Sun Y, Moore MJ, Lin N, Adelalu KF, Meng A, Jian S, Yang L, Li J, Wang H. Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family. BMC Genomics 2017; 18:592. [PMID: 28793854 PMCID: PMC5551029 DOI: 10.1186/s12864-017-3956-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae. RESULTS Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora . Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. CONCLUSION The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales .
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Affiliation(s)
- Yanxia Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | | | - Nan Lin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kole F Adelalu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Aiping Meng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shuguang Jian
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Linsen Yang
- Hubei Key Laboratory of Shennongjia Golden Monkey Conservation Biology, Administration of Shennongjia National Park, Shennongjia, Hubei, China
| | - Jianqiang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Hengchang Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
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Villegente M, Marmey P, Job C, Galland M, Cueff G, Godin B, Rajjou L, Balliau T, Zivy M, Fogliani B, Sarramegna-Burtet V, Job D. A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda. Proteomes 2017; 5:E19. [PMID: 28788068 PMCID: PMC5620536 DOI: 10.3390/proteomes5030019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/13/2022] Open
Abstract
Desiccation tolerance allows plant seeds to remain viable in a dry state for years and even centuries. To reveal potential evolutionary processes of this trait, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda, an understory shrub endemic to New Caledonia that is considered to be the basal extant angiosperm. The present analysis led to the characterization of 415 and 69 proteins from the isolated embryo and endosperm tissues, respectively. The role of these proteins is discussed in terms of protein evolution and physiological properties of the rudimentary, underdeveloped, Amborella embryos, notably considering that the acquisition of desiccation tolerance corresponds to the final developmental stage of mature seeds possessing large embryos.
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Affiliation(s)
- Matthieu Villegente
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851 Nouméa, Nouvelle-Calédonie.
| | - Philippe Marmey
- Institut de recherche pour le développement (IRD), UMR Diversité, Adaptation et Développement des plantes (DIADE), BP A5, 98848 Nouméa Cedex, Nouvelle-Calédonie.
| | - Claudette Job
- Centre National de la Recherche Scientifique (CNRS), CNRS-Université Claude Bernard Lyon-Institut National des Sciences Appliquées-Bayer CropScience (UMR5240), Bayer CropScience, F-69263 Lyon CEDEX 9, France.
| | - Marc Galland
- IJPB, Institut Jean-Pierre Bourgin (Institut National de la Rechercherche Agronomique(INRA), AgroParisTech, CNRS, Université Paris-Saclay) ; « Saclay Plant Sciences (SPS) » - RD10, F-78026 Versailles, France.
| | - Gwendal Cueff
- IJPB, Institut Jean-Pierre Bourgin (Institut National de la Rechercherche Agronomique(INRA), AgroParisTech, CNRS, Université Paris-Saclay) ; « Saclay Plant Sciences (SPS) » - RD10, F-78026 Versailles, France.
- AgroParisTech, Département « Science de la Vie et Santé », Unité de Formation-Recherche en Physiologie végétale, F-75231 Paris, France.
| | - Béatrice Godin
- IJPB, Institut Jean-Pierre Bourgin (Institut National de la Rechercherche Agronomique(INRA), AgroParisTech, CNRS, Université Paris-Saclay) ; « Saclay Plant Sciences (SPS) » - RD10, F-78026 Versailles, France.
- AgroParisTech, Département « Science de la Vie et Santé », Unité de Formation-Recherche en Physiologie végétale, F-75231 Paris, France.
| | - Loïc Rajjou
- IJPB, Institut Jean-Pierre Bourgin (Institut National de la Rechercherche Agronomique(INRA), AgroParisTech, CNRS, Université Paris-Saclay) ; « Saclay Plant Sciences (SPS) » - RD10, F-78026 Versailles, France.
- AgroParisTech, Département « Science de la Vie et Santé », Unité de Formation-Recherche en Physiologie végétale, F-75231 Paris, France.
| | - Thierry Balliau
- Plateforme d'Analyse Protéomique de Paris Sud Ouest (PAPPSO), GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France.
| | - Michel Zivy
- Plateforme d'Analyse Protéomique de Paris Sud Ouest (PAPPSO), GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France.
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851 Nouméa, Nouvelle-Calédonie.
- Institut Agronomique Néo-Calédonien (IAC), Équipe ARBOREAL, Agriculture Biodiversité et Valorisation, BP 73 Port Laguerre, 98890 Païta, Nouvelle-Calédonie.
| | - Valérie Sarramegna-Burtet
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851 Nouméa, Nouvelle-Calédonie.
| | - Dominique Job
- Centre National de la Recherche Scientifique (CNRS), CNRS-Université Claude Bernard Lyon-Institut National des Sciences Appliquées-Bayer CropScience (UMR5240), Bayer CropScience, F-69263 Lyon CEDEX 9, France.
- AgroParisTech, Département « Science de la Vie et Santé », Unité de Formation-Recherche en Physiologie végétale, F-75231 Paris, France.
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Yerramsetty P, Agar EM, Yim WC, Cushman JC, Berry JO. An rbcL mRNA-binding protein is associated with C3 to C4 evolution and light-induced production of Rubisco in Flaveria. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4635-4649. [PMID: 28981775 PMCID: PMC5853808 DOI: 10.1093/jxb/erx264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Nuclear-encoded RLSB protein binds chloroplastic rbcL mRNA encoding the Rubisco large subunit. RLSB is highly conserved across all groups of land plants and is associated with positive post-transcriptional regulation of rbcL expression. In C3 leaves, RLSB and Rubisco occur in all chlorenchyma cell chloroplasts, while in C4 leaves these accumulate only within bundle sheath (BS) chloroplasts. RLSB's role in rbcL expression makes modification of its localization a likely prerequisite for the evolutionary restriction of Rubisco to BS cells. Taking advantage of evolutionarily conserved RLSB orthologs in several C3, C3-C4, C4-like, and C4 photosynthetic types within the genus Flaveria, we show that low level RLSB sequence divergence and modification to BS specificity coincided with ontogeny of Rubisco specificity and Kranz anatomy during C3 to C4 evolution. In both C3 and C4 species, Rubisco production reflected RLSB production in all cell types, tissues, and conditions examined. Co-localization occurred only in photosynthetic tissues, and both proteins were co-ordinately induced by light at post-transcriptional levels. RLSB is currently the only mRNA-binding protein to be associated with rbcL gene regulation in any plant, with variations in sequence and acquisition of cell type specificity reflecting the progression of C4 evolution within the genus Flaveria.
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Affiliation(s)
- Pradeep Yerramsetty
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Erin M Agar
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
| | - Won C Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - James O Berry
- Department of Biological Sciences, State University of New York, Buffalo, NY, USA
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Brewer JS. Stochastic losses of fire-dependent endemic herbs revealed by a 65-year chronosequence of dispersal-limited woody plant encroachment. Ecol Evol 2017. [PMID: 28649349 PMCID: PMC5478063 DOI: 10.1002/ece3.3020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The factors responsible for maintaining diverse groundcover plant communities of high conservation value in frequently burned wet pine savannas are poorly understood. While most management involves manipulating extrinsic factors important in maintaining species diversity (e.g., fire regimes), most ecological theory (e.g., niche theory and neutral theory) examines how traits exhibited by the species promote species coexistence. Furthermore, although many ecologists focus on processes that maintain local species diversity, conservation biologists have argued that other indices (e.g., phylogenetic diversity) are better for evaluating assemblages in terms of their conservation value. I used a null model that employed beta‐diversity calculations based on Raup–Crick distances to test for deterministic herbaceous species losses associated with a 65‐year chronosequence of woody species encroachment within each of three localities. I quantified conservation value of assemblages by measuring taxonomic distinctness, endemism, and floristic quality of plots with and without woody encroachment. Reductions in herb species richness per plot attributable to woody encroachment were largely stochastic, as indicated by a lack of change in the mean or variance in beta‐diversity caused by woody encroachment in the savannas studied here. Taxonomic distinctness, endemism, and floristic quality (when summed across all species) were all greater in areas that had not experienced woody encroachment. However, when corrected for local species richness, only average endemism and floristic quality of assemblages inclusive of herbs and woody plants were greater in areas that had not experienced woody encroachment, due to the more restricted ranges and habitat requirements of herbs. Results suggest that frequent fires maintain diverse assemblages of fire‐dependent herb species endemic to the region. The stochastic loss of plant species, irrespective of their taxonomic distinctness, to woody encroachment suggests that the relevance of niche partitioning or phylogenetic diversity to the management of biodiversity in wet pine savannas is minimal.
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Momtazi AA, Banach M, Pirro M, Katsiki N, Sahebkar A. Regulation of PCSK9 by nutraceuticals. Pharmacol Res 2017; 120:157-169. [PMID: 28363723 DOI: 10.1016/j.phrs.2017.03.023] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 12/19/2022]
Abstract
PCSK9 (proprotein convertase subtilisin kexin type 9) is a liver secretory enzyme that regulates plasma low-density lipoprotein (LDL) cholesterol (LDL-C) levels through modulation of LDL receptor (LDLR) density on the surface of hepatocytes. Inhibition of PCSK9 using monoclonal antibodies can efficiently lower plasma LDL-C, non-high-density lipoprotein cholesterol and lipoprotein (a). PCSK9 inhibition is also an effective adjunct to statin therapy; however, the cost-effectiveness of currently available PCSK9 inhibitors is under question. Nutraceuticals offer a safe and cost-effective option for PCSK9 inhibition. Several nutraceuticals have been reported to modulate PCSK9 levels and exert LDL-lowering activity. Mechanistically, those nutraceuticals that inhibit PCSK9 through a SREBP (sterol-responsive element binding protein)-independent pathway can be more effective in lowering plasma LDL-C levels compared with those inhibiting PCSK9 through the SREBP pathway. The present review aims to collect available data on the nutraceuticals with PCSK9-inhibitory effect and the underlying mechanisms.
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Affiliation(s)
- Amir Abbas Momtazi
- Nanotechnology Research Center, Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maciej Banach
- Department of Hypertension, WAM University Hospital in Lodz, Medical University of Lodz, Zeromskiego 113, Lodz, Poland; Polish Mother's Memorial Hospital Research Institute (PMMHRI), Lodz, Poland
| | - Matteo Pirro
- Unit of Internal Medicine, Angiology and Arteriosclerosis Diseases, Department of Medicine, University of Perugia, Perugia, Italy
| | - Niki Katsiki
- Second Propedeutic Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Hippocration Hospital, Thessaloniki, Greece
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran; Metabolic Research Centre, Royal Perth Hospital, School of Medicine and Pharmacology, University of Western Australia, Perth, Australia.
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Stull GW, Duno de Stefano R, Soltis DE, Soltis PS. Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set. AMERICAN JOURNAL OF BOTANY 2015; 102:1794-813. [PMID: 26507112 DOI: 10.3732/ajb.1500298] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Major relationships within Lamiidae, an asterid clade with ∼40000 species, have largely eluded resolution despite two decades of intensive study. The phylogenetic positions of Icacinaceae and other early-diverging lamiid clades (Garryales, Metteniusaceae, and Oncothecaceae) have been particularly problematic, hindering classification and impeding our understanding of early lamiid (and euasterid) character evolution. METHODS To resolve basal lamiid phylogeny, we sequenced 50 plastid genomes using the Illumina sequencing platform and combined these with available asterid plastome sequence data for more comprehensive phylogenetic analyses. KEY RESULTS Our analyses resolved basal lamiid relationships with strong support, including the circumscription and phylogenetic position of the enigmatic Icacinaceae. This greatly improved basal lamiid phylogeny offers insight into character evolution and facilitates an updated classification for this clade, which we present here, including phylogenetic definitions for 10 new or converted clade names. We also offer recommendations for applying this classification to the Angiosperm Phylogeny Group (APG) system, including the recognition of a reduced Icacinaceae, an expanded Metteniusaceae, and two orders new to APG: Icacinales (Icacinaceae + Oncothecaceae) and Metteniusales (Metteniusaceae). CONCLUSIONS The lamiids possibly radiated from an ancestry of tropical trees with inconspicuous flowers and large, drupaceous fruits, given that these morphological characters are distributed across a grade of lineages (Icacinaceae, Oncothecaceae, Metteniusaceae) subtending the core lamiid clade (Boraginales, Gentianales, Lamiales, Solanales, Vahlia). Furthermore, the presence of similar morphological features among members of Aquifoliales suggests these characters might be ancestral for the Gentianidae (euasterids) as a whole.
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Affiliation(s)
- Gregory W Stull
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525 USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611-7800 USA
| | - Rodrigo Duno de Stefano
- Herbario CICY, Centro de Investigación Científicas de Yucatán A. C., Mérida, Yucatán 97200 Mexico
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525 USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611-7800 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611-7800 USA
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Nascimento Rocha MED, Figueiredo MR, Coelho Kaplan MA, Durst T, Arnason JT. Chemotaxonomy of the Ericales. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Choi KS, Park S. The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae. Gene 2015; 572:214-21. [PMID: 26164759 DOI: 10.1016/j.gene.2015.07.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 06/02/2015] [Accepted: 07/06/2015] [Indexed: 11/26/2022]
Abstract
Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection.
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Affiliation(s)
- Kyoung Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 712-749, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 712-749, South Korea.
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Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The Root of Flowering Plants and Total Evidence. Syst Biol 2015; 64:879-91. [DOI: 10.1093/sysbio/syv028] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
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Allen SE, Stull GW, Manchester SR. Icacinaceae from the eocene of Western North America. AMERICAN JOURNAL OF BOTANY 2015; 102:725-744. [PMID: 26022487 DOI: 10.3732/ajb.1400550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY The Icacinaceae are a pantropical family of trees, shrubs, and climbers with an extensive Paleogene fossil record. Our improved understanding of phylogenetic relationships within the family provides an excellent context for investigating new fossil fruit and leaf material from the Eocene of western North America. METHODS We examined fossils from early and middle Eocene sediments of western Wyoming, northeastern Utah, northwestern Colorado, and Oregon and compared them with extant species of Iodes and other icacinaceous genera as well as previously described fossils of the family. KEY RESULTS Three new fossil species are described, including two based on endocarps (Iodes occidentalis sp. nov. and Icacinicaryites lottii sp. nov.) and one based on leaves (Goweria bluerimensis sp. nov.). The co-occurrence of I. occidentalis and G. bluerimensis suggests these might represent detached organs of a single species. A new genus, Biceratocarpum, is also established for morphologically distinct fossil fruits of Icacinaceae previously placed in Carpolithus. Biceratocarpum brownii gen. et comb. nov. resembles the London Clay species "Iodes" corniculata in possessing a pair of subapical protrusions. CONCLUSIONS These fossils increase our knowledge of Icacinaceae in the Paleogene of North America and highlight the importance of the Northern Hemisphere in the early diversification of the family. They also document interchange with the Eocene flora of Europe and biogeographic connections with modern floras of Africa and Asia, where Icacinaceae are diverse today. The present-day restriction of this family to tropical regions offers ecological implications for the Eocene floras in which they occur.
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Affiliation(s)
- Sarah E Allen
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, Florida 32611 USA Florida Museum of Natural History, P.O. Box 117800, University of Florida, Gainesville, Florida 32611-7800 USA
| | - Gregory W Stull
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, Florida 32611 USA Florida Museum of Natural History, P.O. Box 117800, University of Florida, Gainesville, Florida 32611-7800 USA
| | - Steven R Manchester
- Florida Museum of Natural History, P.O. Box 117800, University of Florida, Gainesville, Florida 32611-7800 USA
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Zhang Q, Feild TS, Antonelli A. Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity. AMERICAN JOURNAL OF BOTANY 2015; 102:566-580. [PMID: 25878090 DOI: 10.3732/ajb.1400527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic incongruence between "gene trees" and "species trees" has been widely acknowledged in phylogenetic research. Conflicts may emerge from several processes including paralogy, hybridization, and incomplete lineage sorting. Although phylogenetic incongruence appears common, its impact on many phylogeny-based analyses remains poorly understood. METHODS We examined the occurrence of phylogenetic conflict between nuclear (ribosome ITS) and plastid (rbcL, trnL-F, rpl20-rps12, and rps16 intron) loci in the ancient angiosperm family Chloranthaceae. Then we investigated how phylogenetic conflict bears on taxonomic classification within the family as well as on inferences on biogeographical history, floral evolution, and measures of phylogenetic diversity (PD). KEY RESULTS We found evidence for significant phylogenetic incongruence between plastid and nuclear data in the genus Hedyosmum. Within Hedyosmum, our results did not support previous subgeneric classification of the genus. Division of sections within subgenus Tafalla was supported by the ITS data but not by the plastid data set. As a consequence, we showed that inferring the evolution of key floral characters and geographical history within Hedyosmum depends on the phylogenetic data used. Both data sets yielded similar PD measures across genera, but we found contrasting PD measures in Hedyosmum, even after correcting for rate heterogeneity. CONCLUSIONS Our study demonstrated that phylogenetic conflict not only affects the inference of organismal relationships but also impacts our understanding of biogeographical history, morphological evolution, and phylogenetic diversity.
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Affiliation(s)
- Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences 541006, Guilin, China
| | - Taylor S Feild
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Alexandre Antonelli
- Gothenburg Botanical Garden and Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
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Wang YH, Jiang WM, Comes HP, Hu FS, Qiu YX, Fu CX. Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio-Pleistocene range dynamics of evergreen forest in subtropical China. THE NEW PHYTOLOGIST 2015; 206:852-67. [PMID: 25639152 DOI: 10.1111/nph.13261] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/02/2014] [Indexed: 05/23/2023]
Abstract
Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest. Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present. Lineages in Southwest vs Central-South-East China diverged through climate/tectonic-induced vicariance of an ancestral southern range during the early Pliocene. Long-term stability in the Southwest contrasts with latitudinal range shifts in the Central-South-East region during the early-to-mid-Pleistocene. Genetic and ENM data strongly suggest refugial persistence in situ at the LGM. Pre-Quaternary environmental changes appear to have had a persistent influence on the population genetic structure of this subtropical WTE forest species. Our findings suggest relative demographic stability of this biome in China over the last glacial-interglacial cycle, in contrast with palaeobiome reconstructions showing that this forest biome retreated to areas of today's tropical South China during the LGM.
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Affiliation(s)
- Yi-Han Wang
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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Costa-Lima JLD, Alves M. Flora da Usina São José, Igarassu, Pernambuco: Erythroxylaceae. RODRIGUÉSIA 2015. [DOI: 10.1590/2175-7860201566118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Erythroxylaceae tem distribuição pantropical e apresenta cerca de 240 espécies circunscritas a quatro gêneros. Apenas Erythroxylum ocorre na região Neotropical e no Brasil são registradas 123 espécies, com maior diversidade na Mata Atlântica, especialmente no Nordeste. A Mata Atlântica do Nordeste do Brasil, considerada a porção mais ameaçada do bioma, é a área com maior diversidade de espécies de Erythroxylum e, embora diversa, a região ainda apresenta deficiência quanto a estudos florísticos e taxonômicos. Desse modo, este estudo objetivou inventariar as espécies de Erythroxylaceae que ocorrem nos fragmentos florestais da Usina São José (Igarassu, Pernambuco), e faz parte do levantamento da flora da área. Este estudo foi baseado na análise morfológica de espécimes coletados na referida área e de espécimes das coleções dos principais herbários do país. Foram registradas oito espécies: Erythroxylum citrifolium, E. mikanii, E. mucronatum, E. nitidum, E. rhodappendiculatum, E. rimosum, E. squamatum e E. subrotundum. Dentre estas, três espécies são registradas aqui pela primeira vez no estado de Pernambuco. Chave para identificação, descrições, ilustrações e comentários sobre hábitat e distribuição geográfica dos táxons são apresentados.
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Montoya-Rodríguez A, Gómez-Favela MA, Reyes-Moreno C, Milán-Carrillo J, González de Mejía E. Identification of Bioactive Peptide Sequences from Amaranth (Amaranthus hypochondriacus) Seed Proteins and Their Potential Role in the Prevention of Chronic Diseases. Compr Rev Food Sci Food Saf 2015; 14:139-158. [DOI: 10.1111/1541-4337.12125] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Alvaro Montoya-Rodríguez
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
- Dept. of Food Science and Human Nutrition; Univ. of Illinois at Urbana-Champaign; IL 61801 U.S.A
| | - Mario A. Gómez-Favela
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
| | - Cuauhtémoc Reyes-Moreno
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
| | - Jorge Milán-Carrillo
- Programa Regional del Noroeste para el Doctorado en Biotecnología, FCQB-UAS; Ciudad Univ; AP 1354, CP 80000 Culiacán Sinaloa México
| | - Elvira González de Mejía
- Dept. of Food Science and Human Nutrition; Univ. of Illinois at Urbana-Champaign; IL 61801 U.S.A
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Molecular phylogeny of Plumbaginaceae with emphasis on Acantholimon Boiss. based on nuclear and plastid DNA sequences in Iran. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Weeks A, Zapata F, Pell SK, Daly DC, Mitchell JD, Fine PVA. To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in "Terebinthaceae" (Anacardiaceae and Burseraceae). Front Genet 2014; 5:409. [PMID: 25506354 PMCID: PMC4247111 DOI: 10.3389/fgene.2014.00409] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/04/2014] [Indexed: 11/13/2022] Open
Abstract
Many angiosperm families are distributed pantropically, yet for any given continent little is known about which lineages are ancient residents or recent arrivals. Here we use a comprehensive sampling of the pantropical sister pair Anacardiaceae and Burseraceae to assess the relative importance of continental vicariance, long-distance dispersal and niche-conservatism in generating its distinctive pattern of diversity over time. Each family has approximately the same number of species and identical stem age, yet Anacardiaceae display a broader range of fruit morphologies and dispersal strategies and include species that can withstand freezing temperatures, whereas Burseraceae do not. We found that nuclear and chloroplast data yielded a highly supported phylogenetic reconstruction that supports current taxonomic concepts and time-calibrated biogeographic reconstructions that are broadly congruent with the fossil record. We conclude that the most recent common ancestor of these families was widespread and likely distributed in the Northern Hemisphere during the Cretaceous and that vicariance between Eastern and Western Hemispheres coincided with the initial divergence of the families. The tempo of diversification of the families is strikingly different. Anacardiaceae steadily accumulated lineages starting in the Late Cretaceous-Paleocene while the majority of Burseraceae diversification occurred in the Miocene. Multiple dispersal- and vicariance-based intercontinental colonization events are inferred for both families throughout the past 100 million years. However, Anacardiaceae have shifted climatic niches frequently during this time, while Burseraceae have experienced very few shifts between dry and wet climates and only in the tropics. Thus, we conclude that both Anacardiaceae and Burseraceae move easily but that Anacardiaceae have adapted more often, either due to more varied selective pressures or greater intrinsic lability.
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Affiliation(s)
- Andrea Weeks
- Department of Biology and Ted R. Bradley Herbarium, George Mason University Fairfax, VA, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, Brown University Providence, RI, USA
| | - Susan K Pell
- United States Botanical Garden Washington, DC, USA
| | - Douglas C Daly
- Institute of Systematic Botany, The New York Botanical Garden Bronx, NY, USA
| | - John D Mitchell
- Institute of Systematic Botany, The New York Botanical Garden Bronx, NY, USA
| | - Paul V A Fine
- Department of Integrative Biology and Jepson and University Herbaria, University of California Berkeley, CA, USA
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Wu Z, Gui S, Quan Z, Pan L, Wang S, Ke W, Liang D, Ding Y. A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC PLANT BIOLOGY 2014; 14:289. [PMID: 25407166 PMCID: PMC4245832 DOI: 10.1186/s12870-014-0289-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 10/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as 'SMRT (Single Molecule, Real-Time) sequencing', has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots. RESULTS The sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region (91,846 bp) and a small single copy region (19,626 bp) separated by two inverted repeat regions (26,064 bp). The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions/contractions within the basal eudicots seem to have occurred independently. CONCLUSIONS Because of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate 'finished' genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions/contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level.
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Affiliation(s)
- Zhihua Wu
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | - Songtao Gui
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | | | - Lei Pan
- />College of Life Sciences, Jianghan University, Wuhan, 430056 China
| | - Shuzhen Wang
- />College of Life Sciences, Huanggang Normal University, Huanggang, 438000 Hubei China
| | - Weidong Ke
- />Wuhan Vegetable Scientific Research Institute, Wuhan National Field Observation & Research Station for Aquatic Vegetables, Wuhan, 430065 China
| | - Dequan Liang
- />Nextomics Biosciences Co., Ltd., Wuhan, 430075 China
| | - Yi Ding
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
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Costa-Lima JLD, Loiola MIB, Jardim JG. Erythroxylaceae no Rio Grande do Norte, Brasil. RODRIGUÉSIA 2014. [DOI: 10.1590/2175-7860201465306] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O presente estudo tem como objetivo contribuir para o conhecimento das espécies de Erythroxylaceae ocorrentes no estado do Rio Grande do Norte. O trabalho tem por base a análise morfológica de materiais depositados em herbários e coletas de campo, além da compilação de dados de literatura. Foram registradas 11 espécies: Erythroxylum barbatum, E. caatingae, E. nummularia, E. passerinum, E. pungens, E. revolutum, E. rimosum, E. simonis, E. squamatum, E. subrotundum e E. vacciniifolium, das quais sete são citadas pela primeira vez no Rio Grande do Norte. Chave para identificação, descrições, ilustrações, dados sobre hábitat, fenologia e distribuição geográfica das espécies são apresentados.
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Comas LH, Callahan HS, Midford PE. Patterns in root traits of woody species hosting arbuscular and ectomycorrhizas: implications for the evolution of belowground strategies. Ecol Evol 2014; 4:2979-90. [PMID: 25247056 PMCID: PMC4161172 DOI: 10.1002/ece3.1147] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/20/2014] [Accepted: 05/27/2014] [Indexed: 11/27/2022] Open
Abstract
Root traits vary enormously among plant species but we have little understanding of how this variation affects their functioning. Of central interest is how root traits are related to plant resource acquisition strategies from soil. We examined root traits of 33 woody species from northeastern US forests that form two of the most common types of mutualisms with fungi, arbuscular mycorrhizas (AM) and ectomycorrhizas (EM). We examined root trait distribution with respect to plant phylogeny, quantifying the phylogenetic signal (K statistic) in fine root morphology and architecture, and used phylogenetically independent contrasts (PICs) to test whether taxa forming different mycorrhizal associations had different root traits. We found a pattern of species forming roots with thinner diameters as species diversified across time. Given moderate phylogenetic signals (K = 0.44-0.68), we used PICs to examine traits variation among taxa forming AM or EM, revealing that hosts of AM were associated with lower branching intensity (r PIC = -0.77) and thicker root diameter (r PIC = -0.41). Because EM evolved relatively more recently and intermittently across plant phylogenies, significant differences in root traits and colonization between plants forming AM and EM imply linkages between the evolution of these biotic interactions and root traits and suggest a history of selection pressures, with trade-offs for supporting different types of associations. Finally, across plant hosts of both EM and AM, species with thinner root diameters and longer specific root length (SRL) had less colonization (r PIC = 0.85, -0.87), suggesting constraints on colonization linked to the evolution of root morphology.
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Affiliation(s)
- Louise H Comas
- Intercollege Graduate Program in Ecology, Department of Horticulture, The Pennsylvania State University103 Tyson Bldg, University Park, Pennsylvania, 16802
- USDA-ARS Water Management Research Unit2150 Centre Avenue, Bldg D Suite 320, Fort Collins, Colorado, 80526
| | - Hilary S Callahan
- Department of Biological Sciences, Barnard College, Columbia University3009 Broadway, New York City, New York, 10027
| | - Peter E Midford
- NESCent2024 W. Main Street, Suite A200, Durham, North Carolina, 27705
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Ajmal Ali M, Gyulai G, Hidvégi N, Kerti B, Al Hemaid FM, Pandey AK, Lee J. The changing epitome of species identification - DNA barcoding. Saudi J Biol Sci 2014; 21:204-31. [PMID: 24955007 PMCID: PMC4061418 DOI: 10.1016/j.sjbs.2014.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/22/2014] [Accepted: 03/23/2014] [Indexed: 01/11/2023] Open
Abstract
The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more.
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Affiliation(s)
- M. Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gábor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Norbert Hidvégi
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Balázs Kerti
- Institute of Genetics and Biotechnology, St. István University, Gödöllo H-2103, Hungary
| | - Fahad M.A. Al Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arun K. Pandey
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Joongku Lee
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305 806, South Korea
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Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE. Another Look at the Root of the Angiosperms Reveals a Familiar Tale. Syst Biol 2014; 63:368-82. [DOI: 10.1093/sysbio/syt108] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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