One thousand plant transcriptomes and the phylogenomics of green plants

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., Soltis, Douglas E., Soltis, Pamela S., Stevenson, Dennis W., Ullrich, Kristian K., Wickett, Norman J., DeGironimo, Lisa, Edger, Patrick P., Jordon-Thaden, Ingrid E., Joya, Steve, Liu, Tao, Melkonian, Michael, 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, Valerie, Caicedo, Ana L., Cannon, Steven B., Cebi, 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., Di Stilio, Veronica S., Ellis, Shona, Fast, Eva, Feja, Nicole, Field, Katie J., Filatov, Dmitry A., Finnegan, Patrick M., Floyd, Sandra K., Fogliani, Bruno, Garcia, Nicolas, Gateble, 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, Konyves, Kalman, 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., Schlosser, Eva-Marie, Sederoff, Heike, Servick, Stein, Sessa, Emily B., Shaw, A. Jonathan, Shaw, Shane W., Sigel, Erin M., Skema, Cynthia, Smith, Alison G., Smithson, Ann, Stewart, C. Neal, Stinchcombe, John R., Szovenyi, 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, Chase, Mark W., Pires, J. 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., Nam-Phuong, Nguyen, 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, Lu-Irving, Patricia, Marx, Hannah E., Qi, Xinshuai, Reardon, Chris R., Sutherland, Brittany L., Tiley, George P., Welles, Shana R., Yu, Rongpei, Zhan, Shing, Gramzow, Lydia, Theissen, Gunter, and Wong, Gane Ka-Shu (2019) One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574. pp. 679-685.

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Abstract

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.

Item ID: 61014
Item Type: Article (Research - C1)
ISSN: 1476-4687
Keywords: adaptive radiation, molecular evolution, phylogenomics, plant evolution
Copyright Information: © The Author(s) 2019. 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.
Funders: Alberta Ministry of Advanced Education and Alberta Innovates AITF/iCORE Strategic Chair, Musea Ventures, The Ministry of Science and Technology of the People’s Republic of China (MOST), State Key Laboratory of Agricultural Genomics (SKLAG), Guangdong Provincial Key Laboratory, School of Environmental Science and Engineering, Sun Yat-Sen University (SESE-SYSU), Shenzhen Municipal Government of China (SZMGC), China National GeneBank (CNGB), Texas Advanced Computing Center (TACC), WestGrid, Compute Canada, National Science Foundation, National Institutes of Health (NIH), USA, Deutsche Forschungsgemeinschaft (DFG), Natural Sciences and Engineering Research Council of Canada Discovery grant
Projects and Grants: Project RES0010334, The National Key Research and Development Program of China (2016YFE0122000), MOST Grant 2015BAD04B01, MOST Grant 2015BAD04B03, SKLAG 2011DQ782025, SESE-SYSU 2011A091000047, SZMGC CXZZ20140421112021913, SZMGC JCYJ20150529150409546, SZMGC JCYJ20150529150505656, NSF DBI-1265383, NSF IOS 0922742, NSF IOS-1339156, NSF DEB 0830009, NSF EF-0629817, NSF EF-1550838, NSF DEB 0733029, NSF DBI 1062335, NSF 1461364, NIH Grant 1R01DA025197, DFG Grant Qu 141/5-1, DFG Grant Qu 141/6-1,, DFG Grant GR 3526/7-1, DFG Grant GR 3526/8-1
Date Deposited: 20 Nov 2019 07:46
FoR Codes: 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis @ 100%
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