Resemblance and Differences in the Feral (C. lanatus subsp. lanatus) and Cultivated Watermelon (C. lanatus subsp. vulgaris) Genomes

Watermelon (C. lanatus) is an important cucurbit crop, accounting for 7% of the worldwide area devoted to vegetable production. The genome of the wild watermelon (C. lanatus subsp. lanatus) PI 296341-FR was sequenced and de novo assembled in this study. The final assembly is 362.1 Mb, representing 86.2% of the watermelon genome. N50 lengths for the scaffold and contigs of the assembled genome are 2.17 Mb and 42.74 kb for the scaffolds and contigs, respectively. A total of 412 scaffolds covering approximately 340 Mb (94% of the assembled genome) were anchored to the 11 watermelon chromosomes. We predicted 23,274 high-confidence protein-coding genes in this wild watermelon genome including 47 NBS R genes. The genome of the cultivated watermelon (C. lanatus subsp. vulgaris) 97103, has been accomplished in our previous study. Preliminary genome comparison was performed between the wild watermelon (C. lanatus subsp. lanatus) PI 296341-FR and the cultivated watermelon (C. lanatus subsp. vulgaris) 97103. Approximately 3.9 Mb SNP variations and 0.7 M Indel variations were identified, affecting ~3000 predicted genes. GO enrichment analysis of these affected genes indicated that several watermelon development and fruit quality related biological process categories were significantly enriched, such as defense response, hormone-mediated signaling pathway, carbohydrate metabolic process, aromatic compound biosynthetic process, fruit development, sucrose metabolic process and carotenoid metabolic process. The whole genome resources of the wild watermelon and the cultivated watermelon will support further evolutionary and comparative genomics studies of the Cucurbitaceaeand shape future efforts in watermelon genetic research and breeding.