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 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.

Keywords: Cochliomyia hominivorax; Calliphoridae; HiC genome; chromosomal assembly; ectoparasite.

Figure 1.

Features along C. hominivorax’s chromosome-scale scaffolds. The gene content of each chromosomal entity is largely conserved between D. melanogaster and C. hominivorax (bottom panel).

Figure 2.

Coverage of female (red) and male (blue) reads across the six chromosomal-scale scaffolds. The male coverage is about half the female coverage for scaffold 315 (bottom-right), an indication that this scaffold is likely from the X chromosome.

Figure 3.

Coverage of female (red) and male (blue) reads across the unplaced scaffolds containing potential Y chromosome regions.

Figure 4.

Identification of putative Y-linked fragments in Cochliomyia hominivorax scaffolds. NWS male and female adult genomic DNA was used as a template to amplify small portions of Y-linked scaffolds identified by the CQ analysis. PCR products were resolved in 2% agarose gels. Male specificity was defined as the presence of a clear amplicon of a distinct size in male but not in female gDNA samples. A map of each of the analyzed scaffolds shows the regions amplified (cyan male, magenta both sexes). ♂ (male), ♀ (female), ntc (no-template control).

Figure 5.

Density of Y-unique regions along the chromosomal-scale scaffolds (in non-overlapping windows of 1.8 Mb). Y-unique regions are continuous regions of 25 bp or more only mapped to by male derived WGS.

Figure 6.

Identification of putative Y-linked genes in Cochliomyia hominivorax scaffolds. NWS male and female adult genomic DNA was used as a template to amplify putative Y-linked genes, by long fragment PCR, identified by the CQ analysis. Male specificity was defined as the presence of a clear amplicon of a distinct size in male but not in female gDNA samples.