1. One thousand plant transcriptomes and the phylogenomics of green plants
- Author
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Leebens, Mack J.H., Graham, S.W, Wong, G.K-S., DeGironimo, L., Edger, P.P., Jordon-Thaden, I.E., Joya, S., Melkonian, B., Miles, N.W., Pokorny Montero, L., Quigley, C., Thomas, P., Villarreal, J.C., Augustin, M.M., Barrett, M.D., Baucom, R.S., Beerling, D.J., Benstein, R.M., Biffin, E., Brockington, S.F., Burge, D.O., Burris, J.N., Burris, K.P., Burtet-Sarramegna, V., Caicedo, A.L., Cannon, S.B., Çebi, Z., Chang, Y., Chater, C., Cheeseman, J.M., Chen, T., Clarke, N.D., Clayton, H., Covshoff, S., Crandall-Stotler, B.J., Cross, H., Determann, R., Dickson, R.C., Di Stilio, V.S., Ellis, S., Fast, E., Feja, N., Field, K.J., Filatov, D.A., Finnegan, P.M., Floyd, S.K., Fogliani, B., GarcÍa, N., Gâteblé, G., Godden, G.T., Goh, Q., Greiner, S., Harkess, A., Heaney, Mike J., Helliwell, K.E., Heyduk, K., Hibberd, J.M., Hodel, R.G.J., Hollingsworth, P.M., Johnson, M.T.J., Jost, R., Joyce, B., Kapralov, M.V., Kazamia, E., Kellogg, E.A., Koch, M.A., Von Konrat, M., Könyves, K., Kutchan, T.M., Lam, V., Larsson, A., Leitch, A.R., Lentz, R., Li, F.-W., Lowe, A.J., Ludwig, M., Manos, P.S., Mavrodiev, E., McCormick, M.K., McKain, M, McLellan, T., McNeal, J., Miller, R., Nelson, M.N., Peng, Y., Ralph, P., Real, D., Riggins, C.W., Ruhsam, M., Sage, R.F., Sakai, A.K., Scascitella, M., Schilling, E.E., Schlösser, E., Sederoff, H., Servick, S., Shaw, A.J., Shaw, S.W., Sigel, E.M., Skema, C., Smith, A.G., Smithson, A., NeilStewart, C., Stinchcombe, J.R., Szövényi, P., Tate, J.A., Tiebel, H., Trapnell, D., Villegente, M., Wang, C., Weller, S.G., Wenzel, M., Weststrand, S., Westwood, J.H., Whigham, D.F., Wulff, A.S., Yang, Y., Zhu, D., Zhuang, C., Zuidof, J., Chase, M.W., Deyholos, M.K., Graham, S.W., Pires, J. Chris, Rothfels, C.J., Chen, C., Chen, L., Cheng, S., Li, J., Li, R., Li, X., Lu, H., Ou, Y., Tan, X., Tang, J., Tian, Z., Wang, F., Wang, J., Wei, X., Wong, G. K.-S., Xu, X., Yan, Z., Yang, F., Zhong, X., Zhou, F., Zhu, Y., Zhang, Y., Yu, J., Barkman, T. J., Carpenter, E. J., Liu, T., Sun, X., Wu, S., Mirarab, S., Nguyen, N., Gitzendanner, M. A., Ayyampalayam, S., Der, J., Matasci, N., Sayyari, E., Soltis, D. E., Soltis, P. S., Stevenson, D. W., Wafula, E. K., Walls, R., Wickett, N. J., De Pamphilis, C. W., Graham, S. W, Leebens-Mack, J. H., Warnow, T., Li, Z., An, H., Arrigo, N., Baniaga, A. E., Galuska, S., Jorgensen, S. A., Kidder, T. I., Kong, H., Lu-Irving, P., Marx, H. E., Qi, X., Reardon, C. R., Sessa, E. B., Sutherland, B. L., Tiley, G. P., Welles, S. R., Yu, R., Zhan, S., Barker, M. S., Porsch, M., Ullrich, K. K., Gramzow, L., Melkonian, M., Nelson, D. R., Theißen, G., Wong, G. K. S., Grosse, I., Rensing, S. A., Quint, M., Institut de sciences exactes et appliquées (ISEA), Université de la Nouvelle-Calédonie (UNC), Apollo - University of Cambridge Repository, National Key Research and Development Program (China), Ministry of Science and Technology of the People's Republic of China, Filatov, D, One Thousand Plant Transcriptomes Initiative, and School of Plant and Environmental Sciences
- Subjects
0106 biological sciences ,Genome evolution ,Nuclear gene ,631/208/212/2306 ,[SDV]Life Sciences [q-bio] ,Viridiplantae ,01 natural sciences ,Genome ,Article ,Evolution, Molecular ,03 medical and health sciences ,Plant evolution ,Phylogenomics ,Databases, Genetic ,Glaucophyta ,631/449/2669 ,631/181/735 ,Plastid ,Phylogeny ,45/90 ,030304 developmental biology ,45/91 ,Adaptive radiation ,0303 health sciences ,631/181/759/2467 ,Multidisciplinary ,biology ,Archaeplastida ,fungi ,Botany ,food and beverages ,Botanik ,15. Life on land ,biology.organism_classification ,Biological Evolution ,Evolutionary biology ,Molecular evolution ,Transcriptome ,Genome, Plant ,010606 plant biology & botany - 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., 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.
- Published
- 2019