Blocks stored synteny results from 72 pair-wised genome comparisons generated from CollinearScan (X. Wang et al., 2006) and McScanX (Y. Wang et al., 2012), including 124,361 blocks and 1,952,225 gene pairs. The nonsynonymous substitution rate (Ka) and synonymous substitution rate (Ks) were calculated for each pair of syntenic genes. Through this data source, research can easily obtain genomic synteny and nucleotide variation information at the single gene, multiple genes, and whole genome scales.