A chromosomal-scale reference genome of the New World Screwworm,Cochliomyia hominivorax

Abstract

The New World Screwworm, Cochliomyia hominivorax (Calliphoridae), is the most important myiasis-causing species in America. Screwworm myiasis is a zoonosis that can cause severe lesions in livestock, domesticated and wild animals, and occasionally in people. Beyond the sanitary problems associated with this species, these infestations negatively impact economic sectors, such as the cattle industry. Here, we present a chromosome-scale assembly of C. hominivorax's genome, organized in 6 chromosome-length and 515 unplaced scaffolds and spanning 534 Mb. There was a clear correspondence between the D. melanogaster linkage groups A-E and the chromosomal-scale scaffolds. Chromosome Quotient (CQ) analysis identified a single scaffold from the X chromosome that contains most of the orthologs of genes that are on the D. melanogaster fourth chromosome (linkage group F or dot chromosome). CQ analysis also identified potential X and Y unplaced scaffolds and genes. Y-linkage for selected regions was confirmed by PCR with male and female DNA. Some of the long chromosome-scale scaffolds include Y-linked sequences, suggesting misassembly of these regions. These resources will provide a basis for future studies aiming at understanding the biology and evolution of this devastating obligate parasite.

Identification and functional analysis of Cochliomyia hominivoraxU6 gene promoters

“…The U6 genes were identified in the screwworm genome by blast analysis of the C. hominivorax chromosome‐scale genome assembly (Scott et al, 2020; Tandonnet et al, 2023) using D. melanogaster U6 genes as a query. U6 candidate genes were found in three clusters, all located in scaffold 470.…”

“…It would appear that these clusters are the same but were misassembled onto separate regions of the scaffold but with an additional U6 gene at the 3 0 end of cluster 3. We noted previously that residual heterozygosity in the inbred strain appears to have led to divergent alleles of some regions of the genome to be assembled onto separate contigs (Scott et al, 2020;Tandonnet et al, 2023).…”

“…Approximately 250 L. cuprina syncytial embryos were injected with each plasmid DNA or plasmid/Cas9 protein mix. Next, larvae that developed from injected embryos and expressed the fluorescent marker were collected, DNA isolated T A B L E 1 Genomic coordinates (Tandonnet et al, 2023) S2).…”

“…Single gRNAs were designed as previously described (Paulo et al, 2019(Paulo et al, , 2022. Briefly, target exons sequences were examined for the presence of protospacer-adjacent motifs (PAMs, sequence NGG-3 0 , where 'N' is any base) using the standalone version of CRISPOR tool (Concordet & Haeussler, 2018) in the context of C. hominivorax genome (GenBank: GCA_004302925.1; Tandonnet et al, 2023).…”

“…We previously established the first protocol to generate site‐specific modifications in the NWS fly genome using the CRISPR/Cas9 system, targeting and disrupting the transformer and brown body (yellow) genes (Paulo et al, 2019). In addition, the recently published whole‐genome assembly of the NWS fly (Scott et al, 2020; Tandonnet et al, 2023) and other ongoing projects could allow the identification of other potential target genes, which could be used in future genetic control programs based on CRISPR/Cas9 (Fresia et al, 2021).…”