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One thousand plant transcriptomes and the phylogenomics of green plants

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dc.contributor.authorLeebens-Mack, James H.en
dc.contributor.authorBarker, Michael S.en
dc.contributor.authorCarpenter, Eric J.en
dc.contributor.authorDeyholos, Michael K.en
dc.contributor.authorGitzendanner, Matthew A.en
dc.contributor.authorGraham, Sean W.en
dc.contributor.authorGrosse, Ivoen
dc.contributor.authorLi, Zhengen
dc.contributor.authorMelkonian, Michaelen
dc.contributor.authorMirarab, Siavashen
dc.contributor.authorPorsch, Martinen
dc.contributor.authorQuint, Marcelen
dc.contributor.authorRensing, Stefan A.en
dc.contributor.authorSoltis, Douglas E.en
dc.contributor.authorSoltis, Pamela S.en
dc.contributor.authorStevenson, Dennis W.en
dc.contributor.authorUllrich, Kristian K.en
dc.contributor.authorWickett, Norman J.en
dc.contributor.authorDeGironimo, Lisaen
dc.contributor.authorEdger, Patrick P.en
dc.contributor.authorJordon-Thaden, Ingrid E.en
dc.contributor.authorJoya, Steveen
dc.contributor.authorLiu, Taoen
dc.contributor.authorMelkonian, Barbaraen
dc.contributor.authorMiles, Nicholas W.en
dc.contributor.authorPokorny, Lisaen
dc.contributor.authorQuigley, Charlotteen
dc.contributor.authorThomas, Philipen
dc.contributor.authorVillarreal, Juan Carlosen
dc.contributor.authorAugustin, Megan M.en
dc.contributor.authorBarrett, Matthew D.en
dc.contributor.authorBaucom, Regina S.en
dc.contributor.authorBeerling, David J.en
dc.contributor.authorBenstein, Ruben Maximilianen
dc.contributor.authorBiffin, Eden
dc.contributor.authorBrockington, Samuel F.en
dc.contributor.authorBurge, Dylan O.en
dc.contributor.authorBurris, Jason N.en
dc.contributor.authorBurris, Kellie P.en
dc.contributor.authorBurtet-Sarramegna, Valerieen
dc.contributor.authorCaicedo, Ana L.en
dc.contributor.authorCannon, Steven B.en
dc.contributor.authorCebi, Zehraen
dc.contributor.authorChang, Yingen
dc.contributor.authorChater, Casparen
dc.contributor.authorCheeseman, John M.en
dc.contributor.authorChen, Taoen
dc.contributor.authorClarke, Neil D.en
dc.contributor.authorClayton, Harmonyen
dc.contributor.authorCovshoff, Sarahen
dc.contributor.authorCrandall-Stotler, Barbara J.en
dc.contributor.authorCross, Hughen
dc.contributor.authordePamphilis, Claude W.en
dc.contributor.authorDer, Joshua P.en
dc.contributor.authorDetermann, Ronen
dc.contributor.authorDickson, Rowan C.en
dc.contributor.authorDi Stilio, Veronica S.en
dc.contributor.authorEllis, Shonaen
dc.contributor.authorFast, Evaen
dc.contributor.authorFeja, Nicoleen
dc.contributor.authorField, Katie J.en
dc.contributor.authorFilatov, Dmitry A.en
dc.contributor.authorFinnegan, Patrick M.en
dc.contributor.authorFloyd, Sandra K.en
dc.contributor.authorFogliani, Brunoen
dc.contributor.authorGarcia, Nicolasen
dc.contributor.authorGateble, Gildasen
dc.contributor.authorGodden, Grant T.en
dc.contributor.authorGoh, Falicia (Qi Yun)en
dc.contributor.authorGreiner, Stephanen
dc.contributor.authorHarkess, Alexen
dc.contributor.authorHeaney, James Mikeen
dc.contributor.authorHelliwell, Katherine E.en
dc.contributor.authorHeyduk, Karolinaen
dc.contributor.authorHibberd, Julian M.en
dc.contributor.authorHodel, Richard G. J.en
dc.contributor.authorHollingsworth, Peter M.en
dc.contributor.authorJohnson, Marc T. J.en
dc.contributor.authorJost, Ricardaen
dc.contributor.authorJoyce, Blakeen
dc.contributor.authorKapralov, Maxim V.en
dc.contributor.authorKazamia, Elenaen
dc.contributor.authorKellogg, Elizabeth A.en
dc.contributor.authorKoch, Marcus A.en
dc.contributor.authorVon Konrat, Matten
dc.contributor.authorKonyves, Kalmanen
dc.contributor.authorKutchan, Toni M.en
dc.contributor.authorLam, Vivienneen
dc.contributor.authorLarsson, Andersen
dc.contributor.authorLeitch, Andrew R.en
dc.contributor.authorLentz, Roswithaen
dc.contributor.authorLi, Fay-Weien
dc.contributor.authorLowe, Andrew J.en
dc.contributor.authorLudwig, Marthaen
dc.contributor.authorManos, Paul S.en
dc.contributor.authorMavrodiev, Evgenyen
dc.contributor.authorMcCormick, Melissa K.en
dc.contributor.authorMcKain, Michaelen
dc.contributor.authorMcLellan, Tracyen
dc.contributor.authorMcNeal, Joel R.en
dc.contributor.authorMiller, Richard E.en
dc.contributor.authorNelson, Matthew N.en
dc.contributor.authorPeng, Yanhuien
dc.contributor.authorRalph, Paula E.en
dc.contributor.authorReal, Danielen
dc.contributor.authorRiggins, Chance W.en
dc.contributor.authorRuhsam, Markusen
dc.contributor.authorSage, Rowan F.en
dc.contributor.authorSakai, Ann K.en
dc.contributor.authorScascitella, Moiraen
dc.contributor.authorSchilling, Edward E.en
dc.contributor.authorSchlosser, Eva-Marieen
dc.contributor.authorSederoff, Heikeen
dc.contributor.authorServick, Steinen
dc.contributor.authorSessa, Emily B.en
dc.contributor.authorShaw, A. Jonathanen
dc.contributor.authorShaw, Shane W.en
dc.contributor.authorSigel, Erin M.en
dc.contributor.authorSkema, Cynthiaen
dc.contributor.authorSmith, Alison G.en
dc.contributor.authorSmithson, Annen
dc.contributor.authorStewart, C. Neal, Jr.en
dc.contributor.authorStinchcombe, John R.en
dc.contributor.authorSzovenyi, Peteren
dc.contributor.authorTate, Jennifer A.en
dc.contributor.authorTiebel, Helgaen
dc.contributor.authorTrapnell, Dorseten
dc.contributor.authorVillegente, Matthieuen
dc.contributor.authorWang, Chun-Nengen
dc.contributor.authorWeller, Stephen G.en
dc.contributor.authorWenzel, Michaelen
dc.contributor.authorWeststrand, Stinaen
dc.contributor.authorWestwood, James H.en
dc.contributor.authorWhigham, Dennis F.en
dc.contributor.authorWu, Shuangxiuen
dc.contributor.authorWulff, Adrien S.en
dc.contributor.authorYang, Yuen
dc.contributor.authorZhu, Danen
dc.contributor.authorZhuang, Cuilien
dc.contributor.authorZuidof, Jenniferen
dc.contributor.authorChase, Mark W.en
dc.contributor.authorPires, J. Chrisen
dc.contributor.authorRothfels, Carl J.en
dc.contributor.authorYu, Junen
dc.contributor.authorChen, Cuien
dc.contributor.authorChen, Lien
dc.contributor.authorCheng, Shifengen
dc.contributor.authorLi, Juanjuanen
dc.contributor.authorLi, Ranen
dc.contributor.authorLi, Xiaen
dc.contributor.authorLu, Haorongen
dc.contributor.authorOu, Yanxiangen
dc.contributor.authorSun, Xiaoen
dc.contributor.authorTan, Xuemeien
dc.contributor.authorTang, Jingboen
dc.contributor.authorTian, Zhijianen
dc.contributor.authorWang, Fengen
dc.contributor.authorWang, Junen
dc.contributor.authorWei, Xiaofengen
dc.contributor.authorXu, Xunen
dc.contributor.authorYan, Zhixiangen
dc.contributor.authorYang, Fanen
dc.contributor.authorZhong, Xiaonien
dc.contributor.authorZhou, Feiyuen
dc.contributor.authorZhu, Yingen
dc.contributor.authorZhang, Yongen
dc.contributor.authorAyyampalayam, Saravanarajen
dc.contributor.authorBarkman, Todd J.en
dc.contributor.authorNam-Phuong Nguyenen
dc.contributor.authorMatasci, Naimen
dc.contributor.authorNelson, David R.en
dc.contributor.authorSayyari, Erfanen
dc.contributor.authorWafula, Eric K.en
dc.contributor.authorWalls, Ramona L.en
dc.contributor.authorWarnow, Tandyen
dc.contributor.authorAn, Hongen
dc.contributor.authorArrigo, Nilsen
dc.contributor.authorBaniaga, Anthony E.en
dc.contributor.authorGaluska, Sallyen
dc.contributor.authorJorgensen, Stacy A.en
dc.contributor.authorKidder, Thomas I.en
dc.contributor.authorKong, Hanghuien
dc.contributor.authorLu-Irving, Patriciaen
dc.contributor.authorMarx, Hannah E.en
dc.contributor.authorQi, Xinshuaien
dc.contributor.authorReardon, Chris R.en
dc.contributor.authorSutherland, Brittany L.en
dc.contributor.authorTiley, George P.en
dc.contributor.authorWelles, Shana R.en
dc.contributor.authorYu, Rongpeien
dc.contributor.authorZhan, Shingen
dc.contributor.authorGramzow, Lydiaen
dc.contributor.authorTheissen, Gunteren
dc.contributor.authorWong, Gane Ka-Shuen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2020-02-24T15:52:59Zen
dc.date.available2020-02-24T15:52:59Zen
dc.date.issued2019-10-31en
dc.description.abstractGreen 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.en
dc.description.adminPublic domain – authored by a U.S. government employeeen
dc.description.notesThe 1KP initiative was funded by the Alberta Ministry of Advanced Education and Alberta Innovates AITF/iCORE Strategic Chair (RES0010334) to G.K.-S.W., Musea Ventures, The National Key Research and Development Program of China (2016YFE0122000), The Ministry of Science and Technology of the People's Republic of China (2015BAD04B01/2015BAD04B03), the State Key Laboratory of Agricultural Genomics (2011DQ782025) and the Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application (2011A091000047). Sequencing activities at BGI were also supported by the Shenzhen Municipal Government of China (CXZZ20140421112021913/JCYJ20150529150409546/JCYJ20150529150505656). Computation support was provided by the China National GeneBank (CNGB), the Texas Advanced Computing Center (TACC), WestGrid and Compute Canada; considerable support, including personnel, computational resources and data hosting, was also provided by the iPlant Collaborative (CyVerse) funded by the National Science Foundation (DBI-1265383), National Science Foundation grants IOS 0922742 (to C.W.d., P.S.S., D.E.S. and J.H.L.-M.), IOS-1339156 (to M.S.B.), DEB 0830009 (to J.H.L.-M., C.W.d., S.W.G. and D.W.S.), EF-0629817 (to S.W.G. and D.W.S.), EF-1550838 (to M.S.B.), DEB 0733029 (to T.W. and J.H.L.-M.), and DBI 1062335 and 1461364 (to T.W.), a National Institutes of Health Grant 1R01DA025197 (to T.M.K., C.W.d. and J.H.L.-M.), Deutsche Forschungsgemeinschaft grants Qu 141/5-1, Qu 141/6-1, GR 3526/7-1, GR 3526/8-1 (to M.Q. and I.G.) and a Natural Sciences and Engineering Research Council of Canada Discovery grant (to S.W.G.). We thank all national, state, provincial and regional resource management authorities, including those of province Nord and province Sud of New Caledonia, for permitting collections of material for this research.en
dc.description.sponsorshipAlberta Ministry of Advanced Education; Alberta Innovates AITF/iCORE Strategic Chair [RES0010334]; Musea Ventures; National Key Research and Development Program of China [2016YFE0122000]; Ministry of Science and Technology of the People's Republic of ChinaMinistry of Science and Technology, China [2015BAD04B01/2015BAD04B03]; State Key Laboratory of Agricultural Genomics [2011DQ782025]; Guangdong Provincial Key Laboratory of core collection of crop genetic resources research and application [2011A091000047]; Shenzhen Municipal Government of China [CXZZ20140421112021913/JCYJ20150529150409546/JCYJ20150529150505656]; National Science FoundationNational Science Foundation (NSF) [DBI-1265383, IOS 0922742, IOS-1339156, DEB 0830009, EF-0629817, EF-1550838, DEB 0733029, DBI 1062335, 1461364]; National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [1R01DA025197]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [Qu 141/5-1, Qu 141/6-1, GR 3526/7-1, GR 3526/8-1]; Natural Sciences and Engineering Research Council of CanadaNatural Sciences and Engineering Research Council of Canadaen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41586-019-1693-2en
dc.identifier.eissn1476-4687en
dc.identifier.issn0028-0836en
dc.identifier.issue7780en
dc.identifier.pmid31645766en
dc.identifier.urihttp://hdl.handle.net/10919/97017en
dc.identifier.volume574en
dc.language.isoenen
dc.rightsCC0 1.0 Universalen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.titleOne thousand plant transcriptomes and the phylogenomics of green plantsen
dc.title.serialNatureen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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