A chromosome-scale genome assembly of the striped fruit fly Zeugodacus scutellatus (Diptera: Tephritidae)

The striped fruit fly Zeugodacus scutellata (Diptera: Tephritidae) is a major cucurbit pest causing over 70% yield losses during outbreaks and poses an ongoing quarantine threat across Asia. To date, the absence of a high-quality reference genome has hindered studies of its invasion dynamics and host adaptations. Here, we present a chromosome-level assembly generated using Illumina short reads, PacBio HiFi long reads, and Hi-C scaffolding. The final assembly is highly contiguous (contig N50 > 10.3 Kb; scaffold N50 > 75.5 Mb) and exhibits >99.3% BUSCO completeness. Annotation identified 13,327 protein-coding genes. We also catalogued repetitive elements, providing insight into genome architecture. All raw sequencing data, assembly files, and annotations have been deposited in public repositories. This resource will enable comparative genomics of Tephritid pests, facilitate population-level analyses of dispersal and adaptation, and support development of molecular tools for monitoring and targeted management of Z. scutellata.