Typical syntenic dot plot between genomes that have undergone shared ancient WGD events. In this example, the synteny plot is between A. lyrata scaffold 1 (x-axis) and A. thaliana chromosome 1 (y-axis). Gray dots represent putative homologous gene pairs, and syntenic gene pairs are plotted with color based on their Ks values. Two significant patterns of synteny are evident. First, these genomes have syntenic regions identified by cyan color that are derived from the divergence of these two taxa, or orthologous blocks. Second, there are smaller magenta-colored synteny blocks that are derived from their shared WGD event and therefore older than orthologous blocks. We observe that these smaller, older blocks overlap with orthologous blocks along one or both of the genomes, which can be used as the basis for screening.
Tang et al. BMC Bioinformatics 2011 12:102 doi:10.1186/1471-2105-12-102