Genome-wide analysis of syntenic gene deletion in the grasses

• Published in: Genome biology and evolution Vol. 4; no. 3; pp. 265 - 277
• Main Authors: Schnable, James C, Freeling, Michael, Lyons, Eric
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-01-2012
• Subjects: Evolution, Molecular; Gene Deletion; Gene Duplication - genetics; Genes; Genome, Plant - genetics; Genomes; Genomics; Grasses; Poaceae - genetics; Polyploidy; Synteny - genetics
• ISSN: 1759-6653; 1759-6653
• DOI: 10.1093/gbe/evs009

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.