One thousand plant transcriptomes and the phylogenomics of green plants

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.

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Item Type:	Article
Authors/Creators:	This paper has 194 authors. You can scroll the list below to see them all or them all. Leebens-Mack, JH Barker, MS Carpenter, EJ Deyholos, MK Gitzendanner, MA Graham, SW Grosse, I Li, Z Melkonian, M Mirarab, S Porsch, M Quint, M Rensing, SA Soltis, DE Soltis, PS Stevenson, DW Ullrich, KK Wickett, NJ DeGironimo, L Edger, PP Jordon-Thaden, IE Joya, S Liu, T Melkonian, B Miles, NW Pokorny, L Quigley, C Thomas, P Villarreal, JC Augustin, MM Barrett, MD Baucom, RS Beerling, DJ Benstein, RM Biffin, E Brockington, SF Burge, DO Burris, JN Burris, KP Burtet-Sarramegna, V Caicedo, AL Cannon, SB Çebi, Z Chang, Y Chater, C Cheeseman, JM Chen, T Clarke, ND Clayton, H Covshoff, S Crandall-Stotler, BJ Cross, H dePamphilis, CW Der, JP Determann, R Dickson, RC Di Stilio, VS Ellis, S Fast, E Feja, N Field, KJ Filatov, DA Finnegan, PM Floyd, SK Fogliani, B García, N Gâteblé, G Godden, GT Goh, FQY Greiner, S Harkess, A Heaney, JM Helliwell, KE Heyduk, K Hibberd, JM Hodel, RGJ Hollingsworth, PM Johnson, MTJ Jost, R Joyce, B Kapralov, MV Kazamia, E Kellogg, EA Koch, MA Von Konrat, M Könyves, K Kutchan, TM Lam, V Larsson, A Leitch, AR Lentz, R Li, F-W Lowe, AJ Ludwig, M Manos, PS Mavrodiev, E McCormick, MK McKain, M McLellan, T McNeal, JR Miller, RE Nelson, MN Peng, Y Ralph, P Real, D Riggins, CW Ruhsam, M Sage, RF Sakai, AK Scascitella, M Schilling, EE Schlösser, E-M Sederoff, H Servick, S Sessa, EB Shaw, AJ Shaw, SW Sigel, EM Skema, C Smith, AG Smithson, A Stewart Jr, CN Stinchcombe, JR Szövényi, P Tate, JA Tiebel, H Trapnell, D Villegente, M Wang, C-N Weller, SG Wenzel, M Weststrand, S Westwood, JH Whigham, DF Wu, S Wulff, AS Yang, Y Zhu, D Zhuang, C Zuidof, J Chase, MW Pires, JC Rothfels, CJ 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, TJ Nguyen, N-P Matasci, N Nelson, DR Sayyari, E Wafula, EK Walls, RL Warnow, T An, H Arrigo, N Baniaga, AE Galuska, S Jorgensen, SA Kidder, TI Kong, H Lu-Irving, P Marx, HE Qi, X Reardon, CR Sutherland, BL Tiley, GP Welles, SR Yu, R Zhan, S Gramzow, L Theißen, G Wong, GK-S
Copyright, Publisher and Additional Information:	© 2019 The Authors. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Keywords:	Adaptive radiation; Molecular evolution; Phylogenomics; Plant evolution
Dates:	Accepted: 12 September 2019 Published: 23 October 2019
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Animal and Plant Sciences (Sheffield) The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Molecular Biology and Biotechnology (Sheffield)
Funding Information:	Funder Grant number EUROPEAN RESEARCH COUNCIL CDREG - 322998
Depositing User:	Symplectic Sheffield
Date Deposited:	12 Nov 2019 10:49
Last Modified:	12 Nov 2019 10:49
Status:	Published
Publisher:	Nature Research
Refereed:	Yes
Identification Number:	10.1038/s41586-019-1693-2
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:153350

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One thousand plant transcriptomes and the phylogenomics of green plants

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