One thousand plant transcriptomes and the phylogenomics of green plants
Creators: name: Leebens-Mack, James H.
name: Barker, Michael S.
name: Carpenter, Eric J.
name: Deyholos, Michael K.
name: Gitzendanner, Matthew A.
name: Graham, Sean W.
name: Grosse, Ivo
name: Li, Zheng
name: Melkonian, Michael
name: Mirarab, Siavash
name: Porsch, Martin
name: Quint, Marcel
name: Rensing, Stefan A.
name: Soltis, Douglas E.
name: Soltis, Pamela S.
name: Stevenson, Dennis W.
name: Ullrich, Kristian K.
name: Wickett, Norman J.
name: DeGironimo, Lisa
name: Edger, Patrick P.
name: Jordon-Thaden, Ingrid E.
name: Joya, Steve
name: Liu, Tao
name: Melkonian, Barbara
name: Miles, Nicholas W.
name: Pokorny, Lisa
name: Quigley, Charlotte
name: Thomas, Philip
name: Villarreal, Juan Carlos
name: Augustin, Megan M.
name: Barrett, Matthew D.
name: Baucom, Regina S.
name: Beerling, David J.
name: Benstein, Ruben Maximilian
name: Biffin, Ed
name: Brockington, Samuel F.
name: Burge, Dylan O.
name: Burris, Jason N.
name: Burris, Kellie P.
name: Burtet-Sarramegna, Valérie
name: Caicedo, Ana L.
name: Cannon, Steven B.
name: Çebi, Zehra
name: Chang, Ying
name: Chater, Caspar
name: Cheeseman, John M.
name: Chen, Tao
name: Clarke, Neil D.
name: Clayton, Harmony
name: Covshoff, Sarah
name: Crandall-Stotler, Barbara J.
name: Cross, Hugh
name: DePamphilis, Claude W.
name: Der, Joshua P.
name: Determann, Ron
name: Dickson, Rowan C.
name: Di Stilio, Verónica S.
name: Ellis, Shona
name: Fast, Eva
name: Feja, Nicole
name: Field, Katie J.
name: Filatov, Dmitry A.
name: Finnegan, Patrick M.
name: Floyd, Sandra K.
name: Fogliani, Bruno
name: García, Nicolás
name: Gâteblé, Gildas
name: Godden, Grant T.
name: Goh, Falicia (Qi Yun)
name: Greiner, Stephan
name: Harkess, Alex
name: Heaney, James Mike
name: Helliwell, Katherine E.
name: Heyduk, Karolina
name: Hibberd, Julian M.
name: Hodel, Richard G. J.
name: Hollingsworth, Peter M.
name: Johnson, Marc T. J.
name: Jost, Ricarda
name: Joyce, Blake
name: Kapralov, Maxim V.
name: Kazamia, Elena
name: Kellogg, Elizabeth A.
name: Koch, Marcus A.
name: Von Konrat, Matt
name: Könyves, Kálmán
name: Kutchan, Toni M.
name: Lam, Vivienne
name: Larsson, Anders
name: Leitch, Andrew R.
name: Lentz, Roswitha
name: Li, Fay-Wei
name: Lowe, Andrew J.
name: Ludwig, Martha
name: Manos, Paul S.
name: Mavrodiev, Evgeny
name: McCormick, Melissa K.
name: McKain, Michael
name: McLellan, Tracy
name: McNeal, Joel R.
name: Miller, Richard E.
name: Nelson, Matthew N.
name: Peng, Yanhui
name: Ralph, Paula
name: Real, Daniel
name: Riggins, Chance W.
name: Ruhsam, Markus
name: Sage, Rowan F.
name: Sakai, Ann K.
name: Scascitella, Moira
name: Schilling, Edward E.
name: Schlösser, Eva-Marie
name: Sederoff, Heike
name: Servick, Stein
name: Sessa, Emily B.
name: Shaw, A. Jonathan
name: Shaw, Shane W.
name: Sigel, Erin M.
name: Skema, Cynthia
name: Smith, Alison G.
name: Smithson, Ann
name: Stewart, C. Neal
name: Stinchcombe, John R.
name: Szövényi, Peter
name: Tate, Jennifer A.
name: Tiebel, Helga
name: Trapnell, Dorset
name: Villegente, Matthieu
name: Wang, Chun-Neng
name: Weller, Stephen G.
name: Wenzel, Michael
name: Weststrand, Stina
name: Westwood, James H.
name: Whigham, Dennis F.
name: Wu, Shuangxiu
name: Wulff, Adrien S.
name: Yang, Yu
name: Zhu, Dan
name: Zhuang, Cuili
name: Zuidof, Jennifer
name: Chase, Mark W.
name: Pires, J. Chris
name: Rothfels, Carl J.
name: Yu, Jun
name: Chen, Cui
name: Chen, Li
name: Cheng, Shifeng
name: Li, Juanjuan
name: Li, Ran
name: Li, Xia
name: Lu, Haorong
name: Ou, Yanxiang
name: Sun, Xiao
name: Tan, Xuemei
name: Tang, Jingbo
name: Tian, Zhijian
name: Wang, Feng
name: Wang, Jun
name: Wei, Xiaofeng
name: Xu, Xun
name: Yan, Zhixiang
name: Yang, Fan
name: Zhong, Xiaoni
name: Zhou, Feiyu
name: Zhu, Ying
name: Zhang, Yong
name: Ayyampalayam, Saravanaraj
name: Barkman, Todd J.
name: Nguyen, Nam-Phuong
name: Matasci, Naim
name: Nelson, David R.
name: Sayyari, Erfan
name: Wafula, Eric K.
name: Walls, Ramona L.
name: Warnow, Tandy
name: An, Hong
name: Arrigo, Nils
name: Baniaga, Anthony E.
name: Galuska, Sally
name: Jorgensen, Stacy A.
name: Kidder, Thomas I.
name: Kong, Hanghui
name: Lu-Irving, Patricia
name: Marx, Hannah E.
name: Qi, Xinshuai
name: Reardon, Chris R.
name: Sutherland, Brittany L.
name: Tiley, George P.
name: Welles, Shana R.
name: Yu, Rongpei
name: Zhan, Shing
name: Gramzow, Lydia
name: Theißen, Günter
name: Wong, Gane Ka-Shu
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/631/181/735
/631/181/759/2467
/631/208/212/2306
/631/449/2669
/45/91
/45/90
article

description: 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.