Comparative And Synteny Analysis Among Watermelon, Melon,and Cucumber Genomes

Watermelon (Citrullus lanatus), cucumber (Cucumis sativus) and melon (Cucumis melo), crops from cucurbitaceae, have important rule among vegetable productions in China as well as the world. Their cultivated areas account for53.18%,53.15%and36.96%of the world devoted by those in China (http://faostat.fao.org/,2011), respectively. As sequencing data and comparative genomics are both developing rapidly, the synteny analysis of cucurbit genomes would enable us to understand the origion, evolution and classification information of these genomes. And it would also help to utilize genentic resources better, and to study the related loci of common traits among these cururbite genomes.To date, genome comparison studies among cucurbit genomes are often limited in cucumis genus, and most of them are based on comparative mapping. Because of the bigger genetic variance inter genera, the poor transferability blocked the application of markers for synteny analysis between watermelon, which is from citrullus genus, and cucumber/melon, which are both from cucumis genus. The completion of the whole genome sequencing projects for watermelon, cucumber and melon enable the comparison among these three genomes with detailed, whole genome sequences. Based on the published genome sequences, we compared the synteny relationships between watermelon, cucumber and melon, inferred the chromosome evolution history of cucumber and melon, and discussed the feasibility of mapping markers among species with the orthologous relationships.The main results are as follows:1. We got1475,1081and984paralogous genes in watermelon, cucumber and melon genomes, whose average value of synonymous mutation rates (Ks) were1.772,1.766and1.703, respectively. The distribution of Ks shows there were no recent whole genome/segmental duplications intra-species.2. With the rule Ks no larger than0.7, we successfully remove those paralogous synteny blocks which are residuals of y event. At last, we got refined data sets with195,211and206synteny blocks from the original344,398and437blocks, with the genome coverage decreased only0.63%,1.56%and2.83%. And it is the first time to get the orthologous blocks between watermelon and melon based on whole genome sequences. This result would be helpful for following studies based on orthologous relationship.3. Based on the paired orthologous blocks, we got orthologs shared by three cucurbit genomes. With watermelon as an out group,17contiguous ancestral regions (CARs) were reconstructed. And the relationship between chromosome1of cucumber (CS01) and chromosome2and12of melon (CM2/CM12) were confirmed, as well as CS03and CM04/CM06, and CS09and CM09/CM10. Fissions in melon instead of fussions in cucumber were suggested in the chromosome evolution history.4. Over85%molecular markers could be transferred from cucumber/melon to watermelon genome with the help of orthologous relationship. This ratio is higher than the successful rate of PCR amplification. We also mapped known markers linked to fusarium wilt or powdery mildew resistance in cucumber or melon to watermelon genome, which could inform investigations in watermelon.