Genome and Transcriptome Sequencing Provides Novel Insights Into Watermelon Evolution, Domestication and Important Biological Processes

Watermelon, Citrullus lanatus var. lanatus, is an important cucurbit crop and is among the top five most consumed fresh fruits. We have generated a high-quality draft genome of the Chinese elite watermelon inbred line 97103. We further performed resequencing of 20 watermelon accessions representing three different C. lanatus subspecies, C. lanatus subsp. lanatus, C. lanatus subsp. mucosospermus, and C. lanatus subsp. vulgaris. Analysis of this resequencing dataset using the 97103 genome as the reference identified approximately 6.8 million SNPs and revealed the extent of genetic diversity and population structure of watermelon germplasm, providing a large resource with great potential for genome manipulation, trait discovery and allele mining. Genomic regions that were preferentially selected during domestication were further identified and they were enriched with genes known to be related to important selected traits. We also found that many disease resistance genes were lost during domestication. Comparative analysis of phloem sap and vascular transcriptomes between watermelon and cucumber revealed that transcript species in vascular bundles between the two cucurbit species were almost identical, whereas the transcripts detected in the phloem sap were largely different. Finally, transcriptome sequencing of fruit flesh and rind during its development identified genes critical to valuable fruit quality traits, such as sugar accumulation and citrulline metabolism.