Transcriptome sequences resolve deep relationships of the grape family

PLoS One. 2013 Sep 17;8(9):e74394. doi: 10.1371/journal.pone.0074394. eCollection 2013.

Abstract

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology
  • Evolution, Molecular
  • Genes, Plant
  • High-Throughput Nucleotide Sequencing*
  • Phylogeny
  • Transcriptome*
  • Vitis / classification*
  • Vitis / genetics*

Grants and funding

This study was funded by grants from the Office of the Smithsonian Undersecretary of Science, the US National Science Foundation (grant DEB 0743474 to S.R. Manchester and J. Wen, and grant DEB 0743499 to J. Gerrath), the Small Grants Program of the National Museum of Natural History of the Smithsonian Institution to JW, and trust funds generated by EAZ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.