Synteny between the B. rapa and A. thaliana genomes. (a) Percent coverage of individual chromosomes showing synteny between B. rapa and A. thaliana. Coverage was calculated as the gene number of an individual chromosome per sum of genes with BLASTP hits. Note that the overall coverage of an individual chromosome for the counterpart genome can exceed 100% because multiple best BLAST hits over the same region are counted. (b) Chromosome correspondence between B. rapa and A. thaliana represented by a dot-plot. Each dot represents a reciprocal best BLASTP match between gene pairs at an E-value cutoff of <E-20. Red dots show regions of synteny with more than 50% gene conservation as identified by DiagHunter. Some Br chromosome orientations have been flipped (A1f, A3f, A7f) to visually correspond to At orientations. Both Br and At have been scaled to occupy the same lengths. Color bars on the upper and left margins of the dot plot indicate individual chromosomes of At and Br, respectively. Black dots on the At chromosomes are centromeres. The color-shaded boxes in the dot plots represent long-range synteny blocks along chromosome pairs. Boxes with the same color are putative triplicated remnants. See Additional data file 3 and the URL cited in Materials and methods for all dot plots and related results, including detailed close-ups of regions of synteny.