Down a Long and Winding Road: Tackling Insect Research Using Long Reads
Long-read data results in telomere to telomere assembly of autosomes and sex chromosomes in Zeugodacus curcurbitae and provides nucleotide-level resolution of sex linked translocations characteristic of the genetic sexing sterile insect technique strain
The melon fly, Zeugodacus cucurbitae, is an oligophagous species of true fruit flies (Diptera: Tephritidae) that attacks agriculturally important cucurbits in its native and introduced ranges. To gain understanding of this species and provide a foundational genomic resource for comparative genomic analyses with other economically important tephritids, we sequenced and assembled the genome of a wildtype melon fly to a chromosome-scale using PacBio HiFi long-read sequencing of the whole genome and Element Aviti short-read sequencing of a chromosome conformation (HiC) library. This resulted in a near gapless assembly of all five autosomes and both the X and Y chromosome. Additional long-read sequence data from a translocated genetic sexing strain for Z. cucurbitae provided nucleotide-level resolution of translocation breakpoints and revealed additional sex-linked genes that may have applications in pest management.