Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)

Eric J. Carpenter, Naim Matasci, Saravanaraj Ayyampalayam, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matthew A. Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Norman J. Wickett, Todd J. Barkmann, Michael S. Barker, James H. Leebens-Mack, Gane Ka Shu Wong

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Background: The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). Findings: This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations. Conclusions: These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages.

Original languageEnglish (US)
Article numbergiz126
JournalGigaScience
Volume8
Issue number10
DOIs
StatePublished - Oct 1 2019

Keywords

  • RNA
  • assemblies
  • contamination
  • genes
  • plants
  • transcriptome completeness

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

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    Carpenter, E. J., Matasci, N., Ayyampalayam, S., Wu, S., Sun, J., Yu, J., Jimenez Vieira, F. R., Bowler, C., Dorrell, R. G., Gitzendanner, M. A., Li, L., Du, W., Ullrich, K., Wickett, N. J., Barkmann, T. J., Barker, M. S., Leebens-Mack, J. H., & Wong, G. K. S. (2019). Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). GigaScience, 8(10), [giz126]. https://doi.org/10.1093/gigascience/giz126