This data supports the manuscript "Integrating classical genetics with chromosome-scale genome assembly to characterize a genetic sexing system in Bactrocera cucurbitae (Diptera: Tephritidae)". The melon fly, Bactrocera cucurbitae, is a destructive agricultural pest and is the subject of strict quarantines that are enforced to prevent its establishment outside of its current geographic range. In addition to quarantine efforts, additional control measures are necessary for its eradication in the case of invasion to agriculturally rich areas. The sterile insect technique (SIT) has been effective in the control of several invertebrate pest species, and is part of a management strategy that regulatory agencies would like to expand to other important pests such as the melon fly.

To develop an SIT program for new species, a genetic sexing strain (GSS), a strain which enables the automation of sorting males from females so that only sterile males are released, is necessary. There exists a GSS for B. cucurbitae in which pupal color is sexually dimorphic where females have a white pupal case and males have a wild type brown pupal case, but its genetic basis is largely unknown, foundational genomic tools for this species are minimal, and information on gene assembly is sparse.

In this study, the B. cucurbitae genome was sequenced, assembled, and placed into chromosome-scale linkage group using linkage information derived from ddRAD sequences from an F4 mapping population.

Using this chromosome-scale assembly and its annotated gene set, a synteny analysis showed a near-perfect relationship between chromosomes in B. cucurbitae and Muller Elements A-E in Drosophila melanogaster. The assembly and linkage map was also used to identify SNP loci very closely linked to the white pupae gene and lays the foundation for the development of this species for its release in SIT programs. This dataset presents data resources supporting this manuscript, including superscaffolding, gene annotation, orthology and synteny analysis.