“One thousand plant transcriptomes and the phylogenomics of green plants”
Nature, vol. 574, no. 7780, 31 October 2019.
SCI 333
Green plants (Viridiplantae) include around 450,000–500,000 species 1 , 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. The One Thousand Plant Transcriptomes Initiative provides a robust phylogenomic framework for examining green plant evolution that comprises the transcriptomes and genomes of diverse species of green plants.
[Description Source: Nature. Published 2019 (7780).]
Authors
Michael Deyholos is a professor of Biology at the University of British Columbia. He received his PhD at McGill University. He applies genetics and genomics to various plant species to investigate the processes of secondary cell wall development, abiotic stress tolerance, plant-microbe interactions. His research subjects include flax (Linum usitatisssimum), hemp (Cannabis sativa), amaranths, and about 1,000 other species.
Together with the other members of the One Thousand Plant Transcriptomes Initiative: James H. Leebens-Mack, Michael S. Barker, Eric J. Carpenter, Michael K. Deyholos, Matthew A. Gitzendanner, Sean W. Graham, Ivo Grosse, Zheng Li, Michael Melkonian, Siavash Mirarab, Martin Porsch, Marcel Quint, Stefan A. Rensing, Douglas E. Soltis, Pamela S. Soltis, Dennis W. Stevenson, Kristian K. Ullrich, Norman J. Wickett, Lisa DeGironimo, Patrick P. Edger, Ingrid E. Jordon-Thaden, Steve Joya, Tao Liu, Barbara Melkonian, Nicholas W. Miles, Lisa Pokorny, Charlotte 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. Burge, 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, Harmony Clayton, Sarah Covshoff, Barbara J. Crandall-Stotler, Hugh Cross, Claude W. dePamphilis, Joshua P. Der, Ron Determann, Rowan C. Dickson, Verónica S. Di Stilio, Shona Ellis, Eva 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 (Qi Yun) Goh, Stephan Greiner, Alex Harkess, James Mike Heaney, Katherine E. Helliwell, Karolina Heyduk, Julian M. Hibberd, Richard G. J. Hodel, Peter M. Hollingsworth, Marc T. J. Johnson, Ricarda Jost, Blake Joyce, Maxim V. Kapralov, Elena Kazamia, Elizabeth A. Kellogg, Marcus A. Koch, Matt Von Konrat, Kálmán Könyves, Toni M. Kutchan, Vivienne Lam, Anders Larsson, Andrew R. Leitch, Roswitha Lentz, Fay-Wei Li, Andrew J. Lowe, Martha Ludwig, Paul S. Manos, Evgeny Mavrodiev, Melissa K. McCormick, Michael McKain, Tracy McLellan, Joel R. McNeal, Richard E. Miller, Matthew N. Nelson, Yanhui Peng, Paula Ralph, Daniel Real, Chance W. Riggins, Markus Ruhsam, Rowan F. Sage, Ann K. Sakai, Moira Scascitella, Edward E. Schilling, Eva-Marie Schlösser, Heike Sederoff, Stein Servick, Emily B. Sessa, A. Jonathan Shaw, Shane W. Shaw, Erin M. Sigel, Cynthia Skema, Alison G. Smith, Ann Smithson, C. Neal Stewart Jr, John R. Stinchcombe, Peter Szövényi, Jennifer A. Tate, Helga Tiebel, Dorset Trapnell, Matthieu Villegente, Chun-Neng Wang, Stephen G. Weller, Michael Wenzel, Stina Weststrand, James H. Westwood, Dennis F. Whigham, Shuangxiu Wu, Adrien S. Wulff, Yu Yang, Dan Zhu, Cuili Zhuang, Jennifer Zuidof, Mark W. Chase, J. Chris Pires, Carl J. Rothfels, Jun Yu, Cui Chen, Li Chen, Shifeng Cheng, Juanjuan Li, Ran Li, Xia Li, Haorong Lu, Yanxiang Ou, Xiao Sun, Xuemei Tan, Jingbo Tang, Zhijian Tian, Feng Wang, Jun Wang, Xiaofeng Wei, Xun Xu, Zhixiang Yan, Fan Yang, Xiaoni Zhong, Feiyu Zhou, Ying Zhu, Yong Zhang, Saravanaraj Ayyampalayam, Todd J. Barkman, Nam-phuong Nguyen, Naim Matasci, David R. Nelson, Erfan Sayyari, Eric K. Wafula, Ramona L. Walls, Tandy Warnow, Hong An, Nils Arrigo, Anthony E. Baniaga, Sally Galuska, Stacy A. Jorgensen, Thomas I. Kidder, Hanghui Kong, Patricia Lu-Irving, Hannah E. Marx, Xinshuai Qi, Chris R. Reardon, Brittany L. Sutherland, George P. Tiley, Shana R. Welles, Rongpei Yu, Shing Zhan, Lydia Gramzow, Günter Theißen & Gane Ka-Shu Wong.
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