摘要：SummaryComparative 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 subspeciesCucumis melossp.agrestisusing single-molecule real-time sequencing, Hi-C, and an ultra-dense genetic map. Comparative genomics analyses identified two targeted genes,UDP-sugar pyrophosphorylaseandα-galactosidase, that were selected during evolution for specific phloem transport of oligosaccharides inCucurbitaceae. 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 uncoverAlkaline/Neutral Invertase(CINV),Sucrose-Phosphatase 2(SPP2),α-galactosidase, andβ-galactosidaseloci 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.Graphical AbstractDisplay OmittedHighlights•A chromosome-scale genome ofCucumis melossp.agrestissubspecies•The work provides insight into oligosaccharides transport inCucurbitaceae•Findings provide insight into the epigenetic regulation of sucrose accumulation in developing fruits•Genetic architectures of sucrose accumulation and gummy stem blight resistanceBiological Sciences; Plant Biology; Genomics
