The pan-grass synteny project (Bioinformatics & Computational Biology )
Schnable, James C¹; Pedersen, Brent J¹; Freeling, Mike¹; Lyons, Eric^1
1 Department of Plant and Microbial Biology; University of California-Berkeley; Berkeley, California, USA 94720

Currently, four grass species are represented by at least one complete genome sequence: brachypodium, maize, rice, and sorghum. These genomes provide a powerful comparative dataset for understanding the evolution of phenotypic differences and differences in chromosomal structure. However, identifying syntenic regions among these genomes is complicated by a whole genome duplication (WGD) event that happened prior to the radiation of the grasses, and a maize specific WGD that happened soon after the divergence of the maize and sorghum lineages.. Potentially, this creates syntenic gene-sets that include ten genes: two genes from brachypodium, rice, and sorghum, and four from maize. However, both fractionation and subfunctionalization occur following a WGD, so many complexities arise. In order to correctly classify syntenic relationships within and among these genomes, we developed an automated system that, for any two genomes, infers syntenic regions by identifying collinear sets of putatively homologous genes, calculates the synonymous mutation (Ks) rates for all protein coding syntenic gene-pairs, merges together small blocks of synteny, and calculates the mean Ks value of these merged blocks. This method permits the unambiguous assignment of every syntenic region between all pair-wise comparisons of these genomes, except for one region in all grass genomes that appears to be undergoing extensive concerted evolution. These pair-wise comparisons and evolutionary event assignments are condensed into datasets that enable researchers to easily find the syntenic orthologs and homeologs of their gene of interest. To make these data readily assessable, links are built into the CoGe suite of web-based comparative genomic tools for rapidly extracting sequence data, and comparing multiple syntenic regions to identify different types of genome evolution including local gene duplication, fractionation, conserved noncoding sequences, transpositions, and inversions, as well as gene annotation errors.

CoGe is publicly available at: http://synteny.cnr.berkeley.edu/CoGe

Introduction for maize whole genome analysis using CoGe: http://synteny.cnr.berkeley.edu/wiki/index.php/Maize_Sorghum_Syntenic_dotplot

Funding acknowledgement: National Science Foundation (NSF)