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One thousand plant transcriptomes and the phylogenomics of green plants

2019; Nature Portfolio; Volume: 574; Issue: 7780 Linguagem: Inglês

10.1038/s41586-019-1693-2

1476-4687

Mack J.H. Leebens, Sean W. Graham, Gane Ka‐Shu Wong, Lisa DeGironimo, Patrick P. Edger, Ingrid Jordon‐Thaden, Steve Joya, Barbara Melkonian, N.W. Miles, Lisa Pokorny, Charles Quigley, Philip Thomas, Juan Carlos Villarreal, Megan M. Augustin, Matthew D. Barrett, Regina S. Baucom, David J. Beerling, Ruben Maximilian Benstein, Ed Biffin, Samuel F. Brockington, Dylan O. Bürge, Jason N. Burris, Kellie P. Burris, Valérie Burtet‐Sarramegna, Ana L. Caicedo, Steven B. Cannon, Zehra Çebi, Ying Chang, Caspar Chater, John M. Cheeseman, Tao Chen, Neil D. Clarke, H. M. Clayton, Sarah Covshoff, Barbara Crandall‐Stotler, H. Z. Cross, Ron O. Determann, Ross Dickson, Verónica S. Di Stilio, Shona Ellis, Eva M. Fast, Nicole Feja, Katie J. Field, Dmitry A. Filatov, Patrick M. Finnegan, Sandra K. Floyd, Bruno Fogliani, Nicolás García, Gildas Gâteblé, Grant T. Godden, Falicia Goh, Stephan Greiner, Alex Harkess, Mike J. Heaney, Katherine E. Helliwell, Karolina Heyduk, J.M. Hibberd, Richard G.J. Hodel, Peter M. Hollingsworth, M.T.J. Johnson, Ricarda Jost, Blake L. Joyce, Maxim V. Kapralov, Elena Kazamia, Elizabeth A. Kellogg, Marcus A. Koch, Matt von Konrat, Kálmán Könyves, Toni M. Kutchan, Victor L. Lam, Anders Larsson, Andrew R. Leitch, Robert J. Lentz, Fay‐Wei Li, Andrew J. Lowe, Martha Ludwig, Paul S. Manos, Evgeny V. Mavrodiev, Melissa McCormick, Michael R. McKain, Tracy McLellan, Joel R. McNeal, Robert G. Miller, Matthew N. Nelson, Peng Yuan, Peter J. Ralph, Daniel Real, Chance W. Riggins, Markus Ruhsam, Rowan F. Sage, A. Sakai, M. Scascitella, Edward E. Schilling, E. Schlösser, Heike Sederoff, Stein Servick, A. Jonathan Shaw, Steven W. Shaw, Erin M. Sigel, Cynthia Skema, Alison G. Smith, Ann Smithson, C. Neilstewart, John R. Stinchcombe, Péter Szövényi, Judith A. Tate, H. Tiebel, Dorset W. Trapnell, Matthieu Villegente, Chun‐Neng Wang, Stephen G. Weller, Michaela Wenzel, Stina Weststrand, James H. Westwood, Dennis F. Whigham, Adrien S. Wulff, Ya Yang, Dan Zhu, Zhuang Chen, J. Zuidof, Mark W. Chase, Michael K. Deyholos, Sean W. Graham, J. Chris Pires, Carl J. Rothfels, Chunyan Chen, Long‐Qing Chen, Shifeng Cheng, J. Li, Rui Li, Xi Li, Henry Horng‐Shing Lu, Yang Ou, Xu Tan, Juan Tang, Zhixi Tian, Fan Wang, Jian Wang, Xiaofeng Wei, Gane Ka‐Shu Wong, Xiaoting Xu, Zhixiang Yan, Fu‐Sheng Yang, Xue Zhong, Fang Zhou, Y. Zhu, Yong Zhang, Jun Yu, Todd J. Barkman, Eric Carpenter, Tao Liu, Xiao Sun, Shuangxiu Wu, Siavash Mirarab, Nam Nguyen, Matthew A. Gitzendanner, Saravanaraj Ayyampalayam, Joshua P. Der, Naim Matasci, Erfan Sayyari, Douglas E. Soltis, Pamela S. Soltis, Dennis Wm. Stevenson, Eric Wafula, Ramona Walls, Norman J. Wickett, Claude W. de Pamphilis, Sean W. Graham, Jim Leebens‐Mack, Tandy Warnow, Zheng Li, Hong An, Nils Arrigo, Anthony E. Baniaga, Sebastian P. Galuska, Stacy A. Jorgensen, Thomas I. Kidder, Hanghui Kong, Patricia Lu‐Irving, Hellmut Marx, Xinshuai Qi, Chris R. Reardon, Emily B. Sessa, B.L. Sutherland, George P. Tiley, Shana R. Welles, Rui Yu, Shing H. Zhan, Michael S. Barker, Martin Porsch, Kristian K Ullrich, Lydia Gramzow, Michael Melkonian, David R. Nelson, Günter Theißen, Gane Ka‐Shu Wong, Ian R. Grosse, Stefan A. Rensing, Marcel Quint,

Plant Pathogens and Resistance

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.