TY - JOUR
T1 - One thousand plant transcriptomes and the phylogenomics of green plants
AU - One Thousand Plant Transcriptomes Initiative
AU - Leebens-Mack, James H.
AU - Barker, Michael S.
AU - Carpenter, Eric J.
AU - Deyholos, Michael K.
AU - Gitzendanner, Matthew A.
AU - Graham, Sean W.
AU - Grosse, Ivo
AU - Li, Zheng
AU - Melkonian, Michael
AU - Mirarab, Siavash
AU - Porsch, Martin
AU - Quint, Marcel
AU - Rensing, Stefan A.
AU - Soltis, Douglas E.
AU - Soltis, Pamela S.
AU - Stevenson, Dennis W.
AU - Ullrich, Kristian K.
AU - Wickett, Norman J.
AU - DeGironimo, Lisa
AU - Edger, Patrick P.
AU - Jordon-Thaden, Ingrid E.
AU - Joya, Steve
AU - Liu, Tao
AU - Melkonian, Barbara
AU - Miles, Nicholas W.
AU - Pokorny, Lisa
AU - Quigley, Charlotte
AU - Thomas, Philip
AU - Villarreal, Juan Carlos
AU - Augustin, Megan M.
AU - Barrett, Matthew D.
AU - Baucom, Regina S.
AU - Beerling, David J.
AU - Benstein, Ruben Maximilian
AU - Biffin, Ed
AU - Brockington, Samuel F.
AU - Burge, Dylan O.
AU - Burris, Jason N.
AU - Burris, Kellie P.
AU - Burtet-Sarramegna, Valérie
AU - Caicedo, Ana L.
AU - Cannon, Steven B.
AU - Çebi, Zehra
AU - Chang, Ying
AU - Chater, Caspar
AU - Cheeseman, John M.
AU - Chen, Tao
AU - Clarke, Neil D.
AU - Riggins, Chance W.
AU - Warnow, Tandy
N1 - Acknowledgements The 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\u2019s 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.
PY - 2019/10/31
Y1 - 2019/10/31
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=85074238403&partnerID=8YFLogxK
U2 - 10.1038/s41586-019-1693-2
DO - 10.1038/s41586-019-1693-2
M3 - Article
C2 - 31645766
AN - SCOPUS:85074238403
SN - 0028-0836
VL - 574
SP - 679
EP - 685
JO - Nature
JF - Nature
IS - 7780
ER -