The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

Abstract Melon (Cucumis melo L.) is an important vegetable crop that has extensive history of cultivation. However, the genome wild and semi-wild melon types can be used for analysis agronomic traits not yet available. Here we report a chromosome-level T2T assembly 821 (C. ssp. agrestis var. acidulus), with two haplotypes ~373 Mb ~364 Mb, respectively. Comparative discovered significant number structural variants (SVs) between melo) agrestis) genomes, including copy variation located in ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected signal associated climacteric ripening identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding cytoplasmic short chain dehydrogenase/reductase, which controls biosynthesis abscisic acid. This study provides valuable genetic resources future research breeding.