A high-quality melon genome provides extensive sequence divergence during melon domestication. Cucumis melo

Melon (Cucumis melo L.) is an important vegetable crop and has an extensive history of cultivation. However, the genome of wild and semi-wild melon used for the analysis of agronomic traits has not been reported. Here, we report a chromosome-level T2T genome assembly for Cucumis melo var. acidulus, a semi-wild melon, with a ~372 Mb genome sequence comprising 27,685 annotated genes. A significant number of structural variants (SVs) between the melo and agrestis genomes were discovered through comparative genome analysis across seven available genomes, including a copy number variation locating on the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected one significant signal associated with climacteric ripening traits, and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, that controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon domestication and breeding.