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One thousand plant transcriptomes and the phylogenomics of green plants

One Thousand Plant Transcriptomes Initiative·2019·Nature
DOI 10.1038/s41586-019-1693-2PMC PMC6872490
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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.

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  • The grasses radiated following a whole-genome duplication, the ~70 M ya Rho WGD.

    “Like most plant families (Barker et al., 2016; Stebbins, 1950; One Thousand Plant Transcriptomes Initiative, 2019), but unlike nearly all animal lineages (Muller, 1925), the grasses radiated following a whole-genome duplication: the ~70 M ya Rho WGD.”

    From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as One Thousand Plant Transcriptomes Initiative, 2019

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Metadata

Authors
Initiative, O. T. P. T.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2019-10-23
Volume
574
Issue
7780
Pages
679-685
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/s41586-019-1693-2
PMC
PMC6872490
Cited by
1,734
References
4
Language
en
Licence

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