Supplemental Fig. 5 Homologous dotplot between Medicago truncatula and Glycine max genomes.

  The best, secondary, and other matched homologous gene pairs output by Blast were dotploted by red, blue, and gray colors in this figure, respectively. The Vitis vinifera 19 chromosomes colored by the 7 eudicot ancestral chromosomes according to previous reports (Jaillon et al. 2007). Genomic orthology and outparalogy chromosome regions were identified and distinguished according to chromosomes breakages, number of colinear genes in homologous regions and synonymous substitution rates (Ks) of homologous blocks. Here, two subgenomes of Glycine max created by SST, which donoted by blue and red circles.