Chromosome-level genome assemblies of two underutilized Mediterranean vegetable melons

Melon (Cucumis melo L.) is an exceptionally polymorphic horticultural species, comprising up to 15 botanical varieties. While sweet melons dominate global markets, vegetable melons—characterized by the absence of sugar accumulation during ripening and typically consumed at the immature stage—are cultivated in small, localized areas and are therefore considered neglected and underutilized crops. In Apulia (Southern Italy), two traditional forms of vegetable melon, locally known as meloncella and barattiere, are cultivated for fresh consumption. The meloncella type has been assigned to the chate botanical variety, whereas the taxonomic status of barattiere remains unresolved. Despite their potential value for breeding, genomic resources for these two vegetable melon types are still lacking. Here, we present high-quality, chromosome-level genome assemblies for both meloncella and barattiere, generated by integrating PacBio HiFi, Oxford Nanopore long-read sequencing, and Illumina Hi-C data. The meloncella genome assembly spans 439.52 Mb across 12 chromosomes, with a scaffold N50 of 29.53 Mb, while the barattiere assembly covers 420.85 Mb with a scaffold N50 of 27.71 Mb. Genome annotation identified 37,175 protein-coding genes in meloncella and 35,338 in barattiere, of which approximately 68% and 74%, respectively, were functionally annotated. Assembly completeness assessed using BUSCO revealed high levels of completeness, encompassing from 96.47 to 99.06% of complete Viridiplantae genes. Phylogenomic inference indicated distinct evolutionary trajectories of meloncella and barattiere and revealed lineage-specific patterns of gene family evolution, providing new insights into their genomic differentiation. These results provide the first chromosome-level genomic resources for two underutilized Mediterranean vegetable melons, establishing a foundation for exploring, conserving, and exploiting their untapped genetic diversity with direct applications in breeding.