Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants

Gane Ka Shu Wong, Douglas E. Soltis, Jim Leebens-Mack, Norman J. Wickett, Michael S. Barker, Yves Van De Peer, Sean W. Graham, Michael Melkonian

Research output: Contribution to journalReview article

2 Scopus citations

Abstract

The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (Cbinf4einf photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.

Original languageEnglish (US)
Pages (from-to)741-765
Number of pages25
JournalAnnual Review of Plant Biology
Volume71
DOIs
StatePublished - Apr 29 2020

Keywords

  • bioprospecting
  • gene family expansions
  • genetic networks
  • paleopolyploidy
  • phylogenomics

ASJC Scopus subject areas

  • Physiology
  • Molecular Biology
  • Plant Science
  • Cell Biology

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  • Cite this

    Wong, G. K. S., Soltis, D. E., Leebens-Mack, J., Wickett, N. J., Barker, M. S., Van De Peer, Y., Graham, S. W., & Melkonian, M. (2020). Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants. Annual Review of Plant Biology, 71, 741-765. https://doi.org/10.1146/annurev-arplant-042916-041040