One thousand plant transcriptomes and the phylogenomics of green plants

One Thousand Plant Transcriptomes Initiative

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)679-685
Number of pages7
JournalNature
Volume574
Issue number7780
DOIs
StatePublished - Oct 31 2019

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Viridiplantae
Transcriptome
Plant Genome
Rhodophyta
Glaucophyta
Genome
Embryophyta
Genes
Ferns
Plastids
Polyploidy
Genomics
Ecosystem
Blood Vessels
History
Research

ASJC Scopus subject areas

  • General

Cite this

One thousand plant transcriptomes and the phylogenomics of green plants. / One Thousand Plant Transcriptomes Initiative.

In: Nature, Vol. 574, No. 7780, 31.10.2019, p. 679-685.

Research output: Contribution to journalArticle

One Thousand Plant Transcriptomes Initiative 2019, 'One thousand plant transcriptomes and the phylogenomics of green plants', Nature, vol. 574, no. 7780, pp. 679-685. https://doi.org/10.1038/s41586-019-1693-2
One Thousand Plant Transcriptomes Initiative. One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 2019 Oct 31;574(7780):679-685. https://doi.org/10.1038/s41586-019-1693-2
One Thousand Plant Transcriptomes Initiative. / One thousand plant transcriptomes and the phylogenomics of green plants. In: Nature. 2019 ; Vol. 574, No. 7780. pp. 679-685.
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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.",
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