Genome-wide analysis of syntenic gene deletion in the grasses

James C. Schnable, Michael Freeling, Eric H Lyons

Research output: Contribution to journalArticle

89 Citations (Scopus)

Abstract

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community.

Original languageEnglish (US)
Pages (from-to)265-277
Number of pages13
JournalGenome Biology and Evolution
Volume4
Issue number3
DOIs
StatePublished - 2012

Fingerprint

gene deletion
Gene Deletion
Poaceae
genome
grass
Genome
grasses
gene
Angiospermae
angiosperm
Genes
genes
genomics
divergence
Radiation
Angiosperms
gene duplication
Gene Duplication
analysis
Genomics

Keywords

  • Gene loss
  • Poaceae
  • Polyploidy
  • Speciation
  • Synteny

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Genome-wide analysis of syntenic gene deletion in the grasses. / Schnable, James C.; Freeling, Michael; Lyons, Eric H.

In: Genome Biology and Evolution, Vol. 4, No. 3, 2012, p. 265-277.

Research output: Contribution to journalArticle

Schnable, James C. ; Freeling, Michael ; Lyons, Eric H. / Genome-wide analysis of syntenic gene deletion in the grasses. In: Genome Biology and Evolution. 2012 ; Vol. 4, No. 3. pp. 265-277.
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