Haplotype-resolved genome assemblies for the New World screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), using the trio binning approach

Authors: Hickner, Paul; Sim, Sheina; Luecke, David; BAILEY, EZRA - North Carolina State University; Saelao, Perot; YUSSEFF-VANEGAS, SOHATH - Orise Fellow; Corpuz, Renee; Bodine, Deanna; Bendele, Kylie; QUINTERO, GLADYS - US Department Of State; Arp, Alex; Tietjen, Mackenzie; Lohmeyer, Kimberly; Olafson, Pia

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2026
Publication Date: 2/28/2026
Citation: Hickner, P.V., Sim, S.B., Luecke, D., Bailey, E., Saelao, P., Yusseff-Vanegas, S.Z., Corpuz, R.L., Bodine, D., Bendele, K.G., Quintero, G., Arp, A.P., Tietjen, M., Sagel, A., Vasquez, M., Geib, S.M., Wiegmann, B.M., Scott, M.J., Lohmeyer, K.H., Olafson, P.U., 2026. Haplotype-resolved genome assemblies for the New World screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), using the trio binning approach. G3 (Bethesda). jkag053
DOI: https://doi.org/10.1093/g3journal/jkag053

Interpretive Summary: The New World screwworm is a major pest of livestock and wildlife in the Americas. The first genome assembly for this species was produced in 2023, and it enabled substantial progress in genetic technologies to improve the sterile insect technique, which is used to eliminate New World screwworm. However, recent advances in sequencing now produce whole genomes with fewer errors, and improvements to computational programs yield more reliable identifications of representative genes within these organisms. Here, we employed a genome analysis approach (trio-binning) that uses DNA from a maternal parent, a paternal parent, and one offspring to produce a refined and improved genome of the New World screwworm. Using a computer algorithm that allows the seamless sharing of outputs with public databases, we identified the genes encoding proteins in this species and made this data publicly available to enhance research by the scientific community. Further, we were able to identify the complete X- and Y-chromosome, which were fragmented in the 2023 assembly. Together, these stark improvements will advance future experiments aimed at improving the sterile insect technique and more broadly understanding the differences between parasitic blow flies.

Technical Abstract: The New World screwworm, Cochliomyia hominivorax, is an obligate parasite of warm-blooded animals and a major pest of livestock and wildlife in the Americas. The first genome assembly for C. hominivorax enabled substantial progress in key areas including population structure, gene expression, and transgenic technologies. However, the first genome was sequenced prior to several technological advances that result in fewer errors and better genome annotations. Here, we used the trio-binning approach to produce a haplotype-resolved genome assembly of C. hominivorax. A single male progeny from the cross of a Yaviza male with a J-06 female was sequenced using PacBio HiFi and scaffolded using Hi-C chromatin conformation. We produced a reference assembly (Chom_ref_2025) by transferring a copy of the X chromosome and mitochondrial genome to the paternal haplotype. Chom_ref_2025 is comprised of five autosomes, two sex chromosomes, the mitogenome, and 75 unplaced scaffolds spanning 455.6 Mb, which is closer to the predicted size based on flow cytometry (443.8 Mb) than the previous assembly of 534.4 Mb. NCBI’s external Eukaryotic Genome Annotation Pipeline (EGAPx) was used to annotate the protein coding and non-coding genes in Chom_ref_2025 and the maternal haplotype. Due to the better resolution of the sex chromosomes and updated genome annotations, this improved assembly will advance future experiments aimed at understanding sex determination, gene expression, and the evolution of parasitism in the Calliphoridae.