Comparative Genomics of the Cucurbitaceae

The genome size for watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (Cuucmis sativus) and pumpkin (Cucurbita pepo) is 425, 454, 367 and 502 Mbp, respectively, and considered medium size as compared with most other crops. Whole-genome duplication is common in angiosperm plants. Research has revealed a paleohexaploidy (ϒ) event in the common ancestor of eudicots after the divergence of monocotyledons and dicotyledons. While analysis of published whole-genome sequences of cucumber, melon and watermelon showed traces of these ancient duplication events, there was not evidence of more recent whole-genome duplications in these species. Analysis of the syntenic relationships among watermelon, cucumber, melon and grape has identified 3543 orthologous relationships covering the watermelon, melon, and cucumber genomes. Comparison of melon and cucumber genomes synteny to detect shorter regions of rearrangements confirmed previously reported ancestral fusions of five melon chromosome pairs in cucumber, and several inter- and intra-chromosome rearrangements between the two species. Sequenced genomes of cucumber, melon and watermelon revealed a comparable range of genes from 23 k to 27 k protein coding genes with an average of four to six exons per gene. Current progress in gene mapping technologies such as optical mapping, which produces maps of large individual DNA molecules, can improve cucurbit comparative genomics to detect large structural variations and DNA rearrangements across the species.