Comparative and evolutionary genomics analyses are the powerful tools to provide mechanistic insights into important agronomic traits. Here, we completed a chromosome-scale assembly of the “neglected” but vital melon subspecies ssp. using single-molecule real-time sequencing, Hi-C, and an ultra-dense genetic map. Comparative genomics analyses identified two targeted genes, and , that were selected during evolution for specific phloem transport of oligosaccharides in . Association analysis of transcriptome and the DNA methylation patterns revealed the epigenetic regulation of sucrose accumulation in developing fruits. We constructed the melon recombinant inbred lines to uncover ( ), ( ), , and loci related to sucrose accumulation and an LRR receptor-like serine/threonine-protein kinase associated with gummy stem blight resistance. This study provides essential genomic resources enabling functional genomics studies and the genomics-informed breeding pipelines for improving the fruit quality and disease resistance traits.
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