Data from: One thousand plant transcriptomes and the phylogenomics of green plants

Green plants (Viridiplantae) include around 450,000–500,000 species1,2of
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.