Phylogenetic tree and examples of homologous gene dotplots in Cucurbitales. A, Phylogenetic relationships of the Cucurbitales plants and V. vinifera. B–G, Identified orthologous and paralogous regions between and within genomes of V. vinifera, C. melo, C. moschata, and B. loranthoides. Dark highlighted boxes represent the identified orthologous and paralogous regions, and the highlighted paralogous regions became lighter as the time of the WGD event gets older. The best BLAST-hits are plotted as red dots, and other hits are plotted as blue dots. The Ks median of collinear gene pairs in homologous regions is marked near to the boxes. The lengths of compared chromosome regions are shown in Mb. H, Species phylogenetic trees for the V. vinifera, C. melo, C. moschata, and B. loranthoides genomes. The red six-pointed star represents the ECH event, and the red, orange, and blue squares represent the CCT, BCT, and CST events, respectively. ECH, core-eudicot-common hexaploidization. I, Three ECH-produced paralogous genes in V. vinifera (V) are denoted V1, V2, and V3, each having four orthologous genes in the B. loranthoides (B) or C. moschata (O) genomes and two in the C. melo (E) genome.