One thousand plant transcriptomes and the phylogenomics of green plants, Marx Hannah E, Chase Mark W, Soltis Douglas E, Soltis Pamela S, Lu-Irving Patricia, Theißen Günter, Di Stilio Verónica S., Leebens-Mack James H., Barker Michael S., Carpenter Eric J., Deyholos Michael K., Gitzendanner Matthew A., Graham Sean W., Grosse Ivo, Li Zheng, Melkonian Michael, Mirarab Siavash, Porsch Martin, Quint Marcel, Rensing Stefan A., Stevenson Dennis W., Ullrich Kristian K., Wickett Norman J., DeGironimo Lisa, Edger Patrick P., Jordon-Thaden Ingrid E., Joya Steve, Liu Tao, Melkonian Barbara, Miles Nicholas W., Pokorny Lisa, Quigley Charlotte, Thomas Philip, Villarreal Juan Carlos, Augustin Megan M., Barrett Matthew D., Baucom Regina S., Beerling David J., Benstein Ruben Maximilian, Biffin Ed, Brockington Samuel F., Burge Dylan O., Burris Jason N., Burris Kellie P., Burtet-Sarramegna Valérie, Caicedo Ana L., Cannon Steven B., Çebi Zehra, Chang Ying, Chater Caspar, Cheeseman John M., Chen Tao, Clarke Neil D., Clayton Harmony, Covshoff Sarah, Crandall-Stotler Barbara J., Cross Hugh, dePamphilis Claude W., Der Joshua P., Determann Ron, Dickson Rowan C., Ellis Shona, Fast Eva, Feja Nicole, Field Katie J., Filatov Dmitry A., Finnegan Patrick M., Floyd Sandra K., Fogliani Bruno, García Nicolás, Gâteblé Gildas, Godden Grant T., Goh Falicia (Qi Yun), Greiner Stephan, Harkess Alex, Heaney James Mike, Helliwell Katherine E., Heyduk Karolina, Hibberd Julian M., Hodel Richard G. J., Hollingsworth Peter M., Johnson Marc T. J., Jost Ricarda, Joyce Blake, Kapralov Maxim V., Kazamia Elena, Kellogg Elizabeth A., Koch Marcus A., Von Konrat Matt, Könyves Kálmán, Kutchan Toni M., Lam Vivienne, Larsson Anders, Leitch Andrew R., Lentz Roswitha, Li Fay-Wei, Lowe Andrew J., Ludwig Martha, Manos Paul S., Mavrodiev Evgeny, McCormick Melissa K., McKain Michael, McLellan Tracy, McNeal Joel R., Miller Richard E., Nelson Matthew N., Peng Yanhui, Ralph Paula, Real Daniel, Riggins Chance W., Ruhsam Markus, Sage Rowan F., Sakai Ann K., Scascitella Moira, Schilling Edward E., Schlösser Eva-Marie, Sederoff Heike, Servick Stein, Sessa Emily B., A. Shaw Jonathan, Shaw Shane W., Sigel Erin M., Skema Cynthia, Smith Alison G., Smithson Ann, C. Stewart Neal, Stinchcombe John R., Szövényi Peter, Tate Jennifer A., Tiebel Helga, Trapnell Dorset, Villegente Matthieu, Wang Chun-Neng, Weller Stephen G., Wenzel Michael, Weststrand Stina, Westwood James H., Whigham Dennis F., Wu Shuangxiu, Wulff Adrien S., Yang Yu, Zhu Dan, Zhuang Cuili, Zuidof Jennifer, J. Pires Chris, Rothfels Carl J., Yu Jun, Chen Cui, Chen Li, Cheng Shifeng, Li Juanjuan, Li Ran, Li Xia, Lu Haorong, Ou Yanxiang, Sun Xiao, Tan Xuemei, Tang Jingbo, Tian Zhijian, Wang Feng, Wang Jun, Wei Xiaofeng, Xu Xun, Yan Zhixiang, Yang Fan, Zhong Xiaoni, Zhou Feiyu, Zhu Ying, Zhang Yong, Ayyampalayam Saravanaraj, Barkman Todd J., Nguyen Nam-phuong, Matasci Naim, Nelson David R., Sayyari Erfan, Wafula Eric K., Walls Ramona L., Warnow Tandy, An Hong, Arrigo Nils, Baniaga Anthony E., Galuska Sally, Jorgensen Stacy A., Kidder Thomas I., Kong Hanghui, Qi Xinshuai, Reardon Chris R., Sutherland Brittany L., Tiley George P., Welles Shana R., Yu Rongpei, Zhan Shing, Gramzow Lydia, Wong Gane Ka-Shu, and Initiative One Thousand P, 2019/10/01, Volume 574, Issue 7780, p.679 - 685 (2019)
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.