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

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 gene expression related to fly behavior and physiology and gene editing 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 haplotype-resolved genome assemblies of C. hominivorax. A single male progeny from the cross of a Panama line male with a production strain female was sequenced using PacBio HiFi and scaffolded using Hi-C chromatin conformation, while Illumina NextSeq 2000 was used for short read sequencing of both parents to facilitate trio-binning. We produced a linear haploid reference assembly by transferring a copy of the X chromosome and mitochondrial genome to the paternal haplotype. This assembly 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 the linear haploid reference and the maternal haplotype assemblies. Due to the better resolution of the sex chromosomes and updated genome annotations, these improved assemblies will advance future experiments aimed at understanding sex determination, gene expression, and the evolution of parasitism in the Calliphoridae.