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 plan..., , # Data from: One thousand plant transcriptomes and the phylogenomics of green plants

Dataset DOI: [10.5061/dryad.rn8pk0pr1](https://doi.org/10.5061/dryad.rn8pk0pr1)

## Description of the data and file structure

The files provided here include all the 14187 multi-copy gene families circumscribed in the onekp analyses. These were built using HMMs created from annotated genes from select genomes. See the paper for a full description. 

* Note that the main phylogenetic analyses reported in the onekp paper are only based on the single-copy gene data available on [https://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/oneKP_capstone_2019](https://datacommons.cyverse.org/browse/iplant/home/shared/commons_repo/curated/oneKP_capstone_2019). (DOI: 10.25739/8m7t-4e85)
* These multi-copy gene families were previously available on [http://jlmwiki.plantbio.uga.edu/onekp/v2/orthogroups](http://jlmwiki.plantbio.uga.edu/onekp/v2/orthogroups) but are no longer available. We m...,