Nuclear and organelle genome assemblies of 5 Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais, and Zhimali, belonging to diverse botanical groups.

The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial, and chloroplast high-quality assemblies of 5 melon (Cucumis melo L.) accessions representing 5 botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25× coverage for 4 of them multiplexed in half of a PromethION flowcell, and 48× coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from 7 to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through Benchmarking Universal Single-Copy Orthologs (BUSCO) and Merqury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Merqury QV values ranging between 41 and 47. We focused on the complex NLR resistance gene regions to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurately targeted assemblies of these regions with significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications.