In the Syn-Dotplots interface, we generated 13,068 genomic synteny dotplots (GSDs) in various forms, including BLAST dotplots (B-GSDs), block dotplots (BB-GSDs), and Ks dotplots (BBK-GSDs), to visualize syntenic blocks (SBs) and identify whole genome duplication (WGD) events (Fig. 3b). B-GSDs show anchor gene pairs and potential SBs with BLAST matching information, while BB-GSDs display inferred SBs. BBK-GSDs integrate Ks values to infer SBs linked to evolutionary events. This method efficiently identifies WGDs during legume diversification. For example, A. duranensis chromosomal regions matched two orthologous SBs in G. max, indicating an additional WGD in G. max post-divergence. Syn-Dotplots also includes localization features for user-friendly analysis.