Leebens-MackBarkerCarpenterEtAl2019

Référence

Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J., Deyholos, M.K., Gitzendanner, M.A., Graham, S.W., Grosse, I., Li, Z., Melkonian, M., Mirarab, S., Porsch, M., Quint, M., Rensing, S.A., Soltis, D.E., Soltis, P.S., Stevenson, D.W., Ullrich, K.K., Wickett, N.J., DeGironimo, L., Edger, P.P., Jordon-Thaden, I.E., Joya, S., Liu, T., Melkonian, B., Miles, N.W., Pokorny, L., Quigley, C., Thomas, P., Villarreal, J.C., Augustin, M.M., Barrett, M.D., Baucom, R.S., Beerling, D.J., Benstein, R.M., Biffin, E., Brockington, S.F., Burge, D.O., Burris, J.N., Burris, K.P., Burtet-Sarramegna, V., Caicedo, A.L., Cannon, S.B., Çebi, Z., Chang, Y., Chater, C., Cheeseman, J.M., Chen, T., Clarke, N.D., Clayton, H., Covshoff, S., Crandall-Stotler, B.J., Cross, H., dePamphilis, C.W., Der, J.P., Determann, R., Dickson, R.C., Di Stilio, V.S., Ellis, S., Fast, E., Feja, N., Field, K.J., Filatov, D.A., Finnegan, P.M., Floyd, S.K., Fogliani, B., García, N., Gâteblé, G., Godden, G.T., Goh, F.Q.Y., Greiner, S., Harkess, A., Heaney, J.M., Helliwell, K.E., Heyduk, K., Hibberd, J.M., Hodel, R.G.J., Hollingsworth, P.M., Johnson, M.T.J., Jost, R., Joyce, B., Kapralov, M.V., Kazamia, E., Kellogg, E.A., Koch, M.A., Von Konrat, M., Könyves, K., Kutchan, T.M., Lam, V., Larsson, A., Leitch, A.R., Lentz, R., Li, F.-W., Lowe, A.J., Ludwig, M., Manos, P.S., Mavrodiev, E., McCormick, M.K., McKain, M., McLellan, T., McNeal, J.R., Miller, R.E., Nelson, M.N., Peng, Y., Ralph, P., Real, D., Riggins, C.W., Ruhsam, M., Sage, R.F., Sakai, A.K., Scascitella, M., Schilling, E.E., Schlösser, E.-M., Sederoff, H., Servick, S., Sessa, E.B., Shaw, A.J., Shaw, S.W., Sigel, E.M., Skema, C., Smith, A.G., Smithson, A., Stewart, C.N., Jr., Stinchcombe, J.R., Szövényi, P., Tate, J.A., Tiebel, H., Trapnell, D., Villegente, M., Wang, C.-N., Weller, S.G., Wenzel, M., Weststrand, S., Westwood, J.H., Whigham, D.F., Wu, S., Wulff, A.S., Yang, Y., Zhu, D., Zhuang, C., Zuidof, J., Chase, M.W., Pires, J.C., Rothfels, C.J., Yu, J., Chen, C., Chen, L., Cheng, S., Li, J., Li, R., Li, X., Lu, H., Ou, Y., Sun, X., Tan, X., Tang, J., Tian, Z., Wang, F., Wang, J., Wei, X., Xu, X., Yan, Z., Yang, F., Zhong, X., Zhou, F., Zhu, Y., Zhang, Y., Ayyampalayam, S., Barkman, T.J., Nguyen, N.-P., Matasci, N., Nelson, D.R., Sayyari, E., Wafula, E.K., Walls, R.L., Warnow, T., An, H., Arrigo, N., Baniaga, A.E., Galuska, S., Jorgensen, S.A., Kidder, T.I., Kong, H., Lu-Irving, P., Marx, H.E., Qi, X., Reardon, C.R., Sutherland, B.L., Tiley, G.P., Welles, S.R., Yu, R., Zhan, S., Gramzow, L., Theißen, G., Wong, G.K.-S., One Thousand Plant Transcriptomes Initiative (2019) One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780):679-685. (Scopus )

Résumé

Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life. © 2019, The Author(s).

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@ARTICLE { Leebens-MackBarkerCarpenterEtAl2019,
    AUTHOR = { Leebens-Mack, J.H. and Barker, M.S. and Carpenter, E.J. and Deyholos, M.K. and Gitzendanner, M.A. and Graham, S.W. and Grosse, I. and Li, Z. and Melkonian, M. and Mirarab, S. and Porsch, M. and Quint, M. and Rensing, S.A. and Soltis, D.E. and Soltis, P.S. and Stevenson, D.W. and Ullrich, K.K. and Wickett, N.J. and DeGironimo, L. and Edger, P.P. and Jordon-Thaden, I.E. and Joya, S. and Liu, T. and Melkonian, B. and Miles, N.W. and Pokorny, L. and Quigley, C. and Thomas, P. and Villarreal, J.C. and Augustin, M.M. and Barrett, M.D. and Baucom, R.S. and Beerling, D.J. and Benstein, R.M. and Biffin, E. and Brockington, S.F. and Burge, D.O. and Burris, J.N. and Burris, K.P. and Burtet-Sarramegna, V. and Caicedo, A.L. and Cannon, S.B. and Çebi, Z. and Chang, Y. and Chater, C. and Cheeseman, J.M. and Chen, T. and Clarke, N.D. and Clayton, H. and Covshoff, S. and Crandall-Stotler, B.J. and Cross, H. and dePamphilis, C.W. and Der, J.P. and Determann, R. and Dickson, R.C. and Di Stilio, V.S. and Ellis, S. and Fast, E. and Feja, N. and Field, K.J. and Filatov, D.A. and Finnegan, P.M. and Floyd, S.K. and Fogliani, B. and García, N. and Gâteblé, G. and Godden, G.T. and Goh, F.Q.Y. and Greiner, S. and Harkess, A. and Heaney, J.M. and Helliwell, K.E. and Heyduk, K. and Hibberd, J.M. and Hodel, R.G.J. and Hollingsworth, P.M. and Johnson, M.T.J. and Jost, R. and Joyce, B. and Kapralov, M.V. and Kazamia, E. and Kellogg, E.A. and Koch, M.A. and Von Konrat, M. and Könyves, K. and Kutchan, T.M. and Lam, V. and Larsson, A. and Leitch, A.R. and Lentz, R. and Li, F.-W. and Lowe, A.J. and Ludwig, M. and Manos, P.S. and Mavrodiev, E. and McCormick, M.K. and McKain, M. and McLellan, T. and McNeal, J.R. and Miller, R.E. and Nelson, M.N. and Peng, Y. and Ralph, P. and Real, D. and Riggins, C.W. and Ruhsam, M. and Sage, R.F. and Sakai, A.K. and Scascitella, M. and Schilling, E.E. and Schlösser, E.-M. and Sederoff, H. and Servick, S. and Sessa, E.B. and Shaw, A.J. and Shaw, S.W. and Sigel, E.M. and Skema, C. and Smith, A.G. and Smithson, A. and Stewart, C.N., Jr. and Stinchcombe, J.R. and Szövényi, P. and Tate, J.A. and Tiebel, H. and Trapnell, D. and Villegente, M. and Wang, C.-N. and Weller, S.G. and Wenzel, M. and Weststrand, S. and Westwood, J.H. and Whigham, D.F. and Wu, S. and Wulff, A.S. and Yang, Y. and Zhu, D. and Zhuang, C. and Zuidof, J. and Chase, M.W. and Pires, J.C. and Rothfels, C.J. and Yu, J. and Chen, C. and Chen, L. and Cheng, S. and Li, J. and Li, R. and Li, X. and Lu, H. and Ou, Y. and Sun, X. and Tan, X. and Tang, J. and Tian, Z. and Wang, F. and Wang, J. and Wei, X. and Xu, X. and Yan, Z. and Yang, F. and Zhong, X. and Zhou, F. and Zhu, Y. and Zhang, Y. and Ayyampalayam, S. and Barkman, T.J. and Nguyen, N.-P. and Matasci, N. and Nelson, D.R. and Sayyari, E. and Wafula, E.K. and Walls, R.L. and Warnow, T. and An, H. and Arrigo, N. and Baniaga, A.E. and Galuska, S. and Jorgensen, S.A. and Kidder, T.I. and Kong, H. and Lu-Irving, P. and Marx, H.E. and Qi, X. and Reardon, C.R. and Sutherland, B.L. and Tiley, G.P. and Welles, S.R. and Yu, R. and Zhan, S. and Gramzow, L. and Theißen, G. and Wong, G.K.-S. and One Thousand Plant Transcriptomes Initiative },
    TITLE = { One thousand plant transcriptomes and the phylogenomics of green plants },
    JOURNAL = { Nature },
    YEAR = { 2019 },
    VOLUME = { 574 },
    NUMBER = { 7780 },
    PAGES = { 679-685 },
    NOTE = { cited By 0 },
    ABSTRACT = { Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life. © 2019, The Author(s). },
    AFFILIATION = { Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Department of Biology, The University of British Columbia Okanagan, Kelowna, BC, Canada; Department of Biology, University of Florida, Gainesville, FL, United States; Florida Museum of Natural History, University of Florida, Gainesville, FL, United States; Department of Botany, University of British Columbia, Vancouver, BC, Canada; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany; Botanical Institute, University of Cologne, Cologne, Germany; Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, United States; Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany; Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany; UF Biodiversity Institute, and UF Genetics Institute, University of Florida, Gainesville, FL, United States; New York Botanical Garden, New York, NY, United States; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany; Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, United States; Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, United States; Department of Horticulture, Michigan State University, East Lansing, MI, United States; Department of Botany, University of Wisconsin-Madison, Madison, WI, United States; Ocean University of China, Qingdao, China; Department of Biological Sciences, University of North Texas, Denton, TX, United States; Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Madrid, Spain; Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), Madrid, Spain; Jodrell Laboratory, Royal Botanic Gardens, Kew, London, United Kingdom; School of Marine Sciences, University of Maine, Orono, ME, United States; Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom; Department of Plant Biology, Laval University, Quebec, Quebec, Canada; Donald Danforth Plant Science Center, St Louis, MO, United States; School of Biological Sciences, The University of Western Australia, Perth, WA, Australia; Kings Park and Botanic Garden, Department of Biodiversity, Conservation and Attractions, Perth, WA, Australia; Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom; Umeå Plant Science Centre, Umeå Universitet, Umeå, Sweden; Australian Centre for Evolutionary Biology and Biodiversity, Environment Institute, School of Earth and Environmental Science, University of Adelaide, Adelaide, SA, Australia; Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom; Royal Botanic Garden Sydney, Sydney, New South Wales, Australia; Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States; Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States; Department of Food Science, University of Tennessee, Knoxville, TN, United States; Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States; Institute for Exact and Applied Sciences, University of New Caledonia, Noumea, New Caledonia; Department of Biology, University of Massachusetts, Amherst, MA, United States; USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, United States; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom; Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States; Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China; Yale-NUS College, Singapore, Singapore; School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia; Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States; Department of Anatomy, University of Otago, Dunedin, New Zealand; Biology Department, Pennsylvania State University, University Park, PA, United States; Department of Biological Science, California State University Fullerton, Fullerton, CA, United States; Atlanta Botanical Garden, Atlanta, GA, United States; Massey University, School of Fundamental Sciences, Palmerston North, New Zealand; Department of Biology, University of Washington, Seattle, WA, United States; Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; Department of Plant Sciences, University of Oxford, Oxford, United Kingdom; School of Biological Sciences, Monash University, Melbourne, Victoria, Australia; Institut Agronomique néo-Calédonien (IAC), Equipe ARBOREAL, Païta, New Caledonia; Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile; Genome Institute of Singapore, Singapore, Singapore; Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom; Marine Biological Association, The Laboratory, Plymouth, United Kingdom; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States; Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada; School of Life Sciences, La Trobe University, Bundoora, VIC, Australia; CyVerse, BIO5 Institute, University of Arizona, Tucson, AZ, United States; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; University of Missouri, St Louis, St Louis, MO, United States; Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Botanic Garden and Herbarium Heidelberg, University of Heidelberg, Heidelberg, Germany; The Field Museum, Chicago, IL, United States; Royal Horticultural Society Garden Wisley, Woking, United Kingdom; University of Reading Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom; Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden; School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom; Boyce Thompson Institute, Cornell University, Ithaca, NY, United States; Environment Institute, School of Biological Science, University of Adelaide, Adelaide, SA, Australia; Department of Biology, Duke University, Durham, NC, United States; Smithsonian Environmental Research Center, Edgewater, MD, United States; Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States; School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa; Department of Ecology, Evolution and Organismal Biology, Kennesaw State University, Kennesaw, GA, United States; Flower Diversity Institute, Arvada, CO, United States; CSIRO Agriculture and Food, Perth, WA, Australia; Millennium Seed Bank, Wakehurst, Royal Botanic Gardens, Kew, Ardingly, United Kingdom; The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia; Centers for Disease Control and Prevention, Atlanta, GA, United States; Department of Primary Industries and Regional Development, Perth, WA, Australia; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Ecology and Evolutionary Biology, The University of Toronto, Ontario, Canada; Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States; Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States; Manoa, Honolulu, HI, United States; Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States; Morris Arboretum of the University of Pennsylvania, Philadelphia, PA, United States; Koffler Scientific Reserve, University of Toronto, King City, ON, Canada; Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland; National Taiwan University, Institute of Ecology and Evolutionary Biology, Department of Life Science, Taipei, Taiwan; Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden; Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, United States; CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, China; College of Life Science, Qingdao Agricultural University, Qingdao, China; Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia; Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, MO, United States; Department of Zoology, University of British Columbia, Vancouver, BC, Canada; University Herbarium and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States; Beijing Genomics Institute-Wuhan, Wuhan, China; BGI-Shenzhen, Shenzhen, China; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; Huahan Gene, Shenzhen, China; MGI, BGI-Shenzhen, Shenzhen, China; Allwegene Technology, Beijing, China; iCarbonX, Shenzhen, China; Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States; Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, United States; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States; Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, United States; Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, United States; Department of Computer Science, University of Illinois, Urbana-Champaign, Urbana, IL, United States; Division of Biological Sciences, University of Missouri, Columbia, MO, United States; Arizona Research Laboratories, University of Arizona, Tucson, AZ, United States; Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China; Department of Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany; Department of Medicine, University of Alberta, Edmonton, AB, Canada; Department of Plant Biology, University of Georgia, Athens, GA, United States },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1038/s41586-019-1693-2 },
    SOURCE = { Scopus },
    URL = { https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074238403&doi=10.1038%2fs41586-019-1693-2&partnerID=40&md5=73061669590cf8005e071a709e882b05 },
}

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