Whole Genome Comparisons with Oryza and Brachypodium using CoGe and SynMap

Of the more than 30 plant genomes currently available, the Poaceae represents the most heavily sample family of plants.  Currently, there are five publicly available high-quality grass genomes each from a different genera: Zea, Sorghum, Setaria, Oryza, and Brachypodium.  Here, we focus on comparing the genomes of Oryza sativa and Brachypodium distachyon using CoGe’s tool SynMap.  SynMap generates whole genome syntenic dotplots and makes available a variety of options for modifying its visualization scheme, identifying subsets of genes, and characterize large-scale evolutionary events such as chromosome fusions (a reoccurring process in the evolution of the Brachypodium genome).  This includes measuring the evolutionary distances between syntenic gene pairs in order to evaluate whether identified sytnenic regions are derived from the divergence of these lineages (orthologs) or from a shared whole genome duplication event (out-paralogs), and evaluating those regions for gene loss through high-resolution sequence analysis.  In addition, SynMap incorporates an additional algorithm, Quota Align, which can screen syntenic regions and select those giving a best ratio of coverage.  This permits the rapid identification of an orthologous syntenic gene sets between any two genomes.  Combined, SynMap utilization of visualization and advanced comparative analytical tools permits the rapid characterization of syntenic genes and genomic regions between any two genomes in CoGe’s system.

CoGe and SynMap are available at:  http://genomevolution.org