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  One thousand plant transcriptomes and the phylogenomics of green plants

Leebens-Mack, J. H., Barker, M. S., Carpenter, E. J., Deyholos, M. K., Gitzendanner, M. A., Graham, S. W., et al. (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685. doi:10.1038/s41586-019-1693-2.

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Leebens-Mack, James H.1, Author
Barker, Michael S.1, Author
Carpenter, Eric J.1, Author
Deyholos, Michael K.1, Author
Gitzendanner, Matthew A.1, Author
Graham, Sean W.1, Author
Grosse, Ivo1, Author
Li, Zheng1, Author
Melkonian, Michael1, Author
Mirarab, Siavash1, Author
Porsch, Martin1, Author
Quint, Marcel1, Author
Rensing, Stefan A.1, Author
Soltis, Douglas E.1, Author
Soltis, Pamela S.1, Author
Stevenson, Dennis W.1, Author
Ullrich, Kristian K.1, Author
Wickett, Norman J.1, Author
DeGironimo, Lisa1, Author
Edger, Patrick P.1, Author
Jordon-Thaden, Ingrid E.1, AuthorJoya, Steve1, AuthorLiu, Tao1, AuthorMelkonian, Barbara1, AuthorMiles, Nicholas W.1, AuthorPokorny, Lisa1, AuthorQuigley, Charlotte1, AuthorThomas, Philip1, AuthorVillarreal, Juan Carlos1, AuthorAugustin, Megan M.1, AuthorBarrett, Matthew D.1, AuthorBaucom, Regina S.1, AuthorBeerling, David J.1, AuthorBenstein, Ruben Maximilian1, AuthorBiffin, Ed1, AuthorBrockington, Samuel F.1, AuthorBurge, Dylan O.1, AuthorBurris, Jason N.1, AuthorBurris, Kellie P.1, AuthorBurtet-Sarramegna, Valérie1, AuthorCaicedo, Ana L.1, AuthorCannon, Steven B.1, AuthorÇebi, Zehra1, AuthorChang, Ying1, AuthorChater, Caspar1, AuthorCheeseman, John M.1, AuthorChen, Tao1, AuthorClarke, Neil D.1, AuthorClayton, Harmony1, AuthorCovshoff, Sarah1, AuthorCrandall-Stotler, Barbara J.1, AuthorCross, Hugh1, AuthordePamphilis, Claude W.1, AuthorDer, Joshua P.1, AuthorDetermann, Ron1, AuthorDickson, Rowan C.1, AuthorStilio, Di1, AuthorS., Verónica1, AuthorEllis, Shona1, AuthorFast, Eva1, AuthorFeja, Nicole1, AuthorField, Katie J.1, AuthorFilatov, Dmitry A.1, AuthorFinnegan, Patrick M.1, AuthorFloyd, Sandra K.1, AuthorFogliani, Bruno1, AuthorGarcía, Nicolás1, AuthorGâteblé, Gildas1, AuthorGodden, Grant T.1, AuthorGoh, Falicia (Qi Yun)1, AuthorGreiner, S.2, Author              Harkess, Alex1, AuthorHeaney, James Mike1, AuthorHelliwell, Katherine E.1, AuthorHeyduk, Karolina1, AuthorHibberd, Julian M.1, AuthorHodel, Richard G. J.1, AuthorHollingsworth, Peter M.1, AuthorJohnson, Marc T. J.1, AuthorJost, Ricarda1, AuthorJoyce, Blake1, AuthorKapralov, Maxim V.1, AuthorKazamia, Elena1, AuthorKellogg, Elizabeth A.1, AuthorKoch, Marcus A.1, AuthorVon Konrat, Matt1, AuthorKönyves, Kálmán1, AuthorKutchan, Toni M.1, AuthorLam, Vivienne1, AuthorLarsson, Anders1, AuthorLeitch, Andrew R.1, AuthorLentz, Roswitha1, AuthorLi, Fay-Wei1, AuthorLowe, Andrew J.1, AuthorLudwig, Martha1, AuthorManos, Paul S.1, AuthorMavrodiev, Evgeny1, AuthorMcCormick, Melissa K.1, AuthorMcKain, Michael1, AuthorMcLellan, Tracy1, AuthorMcNeal, Joel R.1, AuthorMiller, Richard E.1, AuthorNelson, Matthew N.1, AuthorPeng, Yanhui1, AuthorRalph, Paula1, AuthorReal, Daniel1, AuthorRiggins, Chance W.1, AuthorRuhsam, Markus1, AuthorSage, Rowan F.1, AuthorSakai, Ann K.1, AuthorScascitella, Moira1, AuthorSchilling, Edward E.1, AuthorSchlösser, Eva-Marie1, AuthorSederoff, Heike1, AuthorServick, Stein1, AuthorSessa, Emily B.1, AuthorShaw, A. Jonathan1, AuthorShaw, Shane W.1, AuthorSigel, Erin M.1, AuthorSkema, Cynthia1, AuthorSmith, Alison G.1, AuthorSmithson, Ann1, AuthorStewart, C. Neal1, AuthorStinchcombe, John R.1, AuthorSzövényi, Peter1, AuthorTate, Jennifer A.1, AuthorTiebel, Helga1, AuthorTrapnell, Dorset1, AuthorVillegente, Matthieu1, AuthorWang, Chun-Neng1, AuthorWeller, Stephen G.1, AuthorWenzel, Michael1, AuthorWeststrand, Stina1, AuthorWestwood, James H.1, AuthorWhigham, Dennis F.1, AuthorWu, Shuangxiu1, AuthorWulff, Adrien S.1, AuthorYang, Yu1, AuthorZhu, Dan1, AuthorZhuang, Cuili1, AuthorZuidof, Jennifer1, AuthorChase, Mark W.1, AuthorPires, J. Chris1, AuthorRothfels, Carl J.1, AuthorYu, Jun1, AuthorChen, Cui1, AuthorChen, Li1, AuthorCheng, Shifeng1, AuthorLi, Juanjuan1, AuthorLi, Ran1, AuthorLi, Xia1, AuthorLu, Haorong1, AuthorOu, Yanxiang1, AuthorSun, Xiao1, AuthorTan, Xuemei1, AuthorTang, Jingbo1, AuthorTian, Zhijian1, AuthorWang, Feng1, AuthorWang, Jun1, AuthorWei, Xiaofeng1, AuthorXu, Xun1, AuthorYan, Zhixiang1, AuthorYang, Fan1, AuthorZhong, Xiaoni1, AuthorZhou, Feiyu1, AuthorZhu, Ying1, AuthorZhang, Yong1, AuthorAyyampalayam, Saravanaraj1, AuthorBarkman, Todd J.1, AuthorNguyen, Nam-phuong1, AuthorMatasci, Naim1, AuthorNelson, David R.1, AuthorSayyari, Erfan1, AuthorWafula, Eric K.1, AuthorWalls, Ramona L.1, AuthorWarnow, Tandy1, AuthorAn, Hong1, AuthorArrigo, Nils1, AuthorBaniaga, Anthony E.1, AuthorGaluska, Sally1, AuthorJorgensen, Stacy A.1, AuthorKidder, Thomas I.1, AuthorKong, Hanghui1, AuthorLu-Irving, Patricia1, AuthorMarx, Hannah E.1, AuthorQi, Xinshuai1, AuthorReardon, Chris R.1, AuthorSutherland, Brittany L.1, AuthorTiley, George P.1, AuthorWelles, Shana R.1, AuthorYu, Rongpei1, AuthorZhan, Shing1, AuthorGramzow, Lydia1, AuthorTheißen, Günter1, AuthorWong, Gane Ka-Shu1, AuthorInitiative, One Thousand Plant Transcriptomes1, Author more..
1external, ou_persistent22              
2Cytoplasmic and Evolutionary Genetics, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753324              


Free keywords: -
 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.


Language(s): eng - English
 Dates: 2019
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1038/s41586-019-1693-2
Other: Leebens-Mack2019
 Degree: -



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Title: Nature
Source Genre: Journal
Publ. Info: -
Pages: - Volume / Issue: 574 (7780) Sequence Number: - Start / End Page: 679 - 685 Identifier: ISBN: 1476-4687