Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs

Abstract

The New World Screwworm fly, Cochliomyia hominivorax, is a major pest of livestock in South America and Caribbean. However, few genomic resources have been available for this species. A genome of 534 Mb was assembled from long read PacBio DNA sequencing of DNA from a highly inbred strain. Analysis of molecular evolution identified 40 genes that are likely under positive selection. Developmental RNA-seq analysis identified specific genes associated with each stage. We identify and analyze the expression of genes that are likely important for host-seeking behavior (chemosensory), development of larvae in open wounds in warm-blooded animals (heat shock protein, immune response) and for building transgenic strains for genetic control programs including gene drive (sex determination, germline). This study will underpin future experiments aimed at understanding the parasitic lifestyle of the screwworm fly and greatly facilitate future development of strains for efficient systems for genetic control of screwworm.

Physiological and molecular correlates of the screwworm fly attraction to wound and animal odors

“…A total of 10,442 genes were expressed in the antennae (Supplemental file 1 ), of which 114 were annotated as chemosensory genes (55 ORs, 15 GRs, 21 IRs and 23 OBPs). It is worth mentioning that these numbers are lower than those we reported in whole genome annotation 30 , and simply reflect the fact that some of these genes are expressed in other tissues such as legs and mouth parts, and/or at different developmental stages. A total of 85 genes were differentially expressed (DE) between the two sexes (Fig.…”

“…Phylogenetic analysis of chemosensory genes. Phylogenetic relationships among C. hominivorax 30 and D. melanogaster 40,76,77 chemosensory genes were estimated by first conducting a multiple protein alignment for each gene family using default parameters in ClustalX v2.1 78 . Alignments were visually inspected and then used for maximum likelihood estimation in RAxML v8.2.11 with the PROTGAMMAAUTO model option and 500 bootstrap replications 79 .…”

“…First, we measured the olfactory sensitivity of C. hominivorax males, virgin or gravid females to the constituent compounds of swormlure-4 . Next, leveraging the newly sequenced genome assembly of this fly 30 , we isolated and analyzed the antennal transcriptome by RNA-Sequencing to gain insights into the molecular basis of olfaction in male and female screwworm flies. Antennal olfactory sensitivity is the outcome from the binding of odorants with the members of three divergent protein families—odorant receptors (ORs), ionotropic receptors (IRs), and gustatory receptors (GRs)—together referred as chemosensory gene families 31 .…”

“…Antennal olfactory sensitivity is the outcome from the binding of odorants with the members of three divergent protein families—odorant receptors (ORs), ionotropic receptors (IRs), and gustatory receptors (GRs)—together referred as chemosensory gene families 31 . We previously identified 79 ORs, 84 GRs, 88 IRs and 51 odorant binding proteins (OBPs) in the screwworm genome 30 . The birth and diversification of these gene families 32 , together with the functional characterization of candidate genes—such as those differentially expressed between sexes, or physiological stages of female—offers the potential to isolate and identify chemicals that are highly effective and selective 4 .…”

Using Moderate Transgene Expression to Improve the Genetic Sexing System of the Australian Sheep Blow Fly Lucilia cuprina

“…The Lsbnk promoter used in this study to drive tTA expression was obtained from L. sericata by a PCR-based genome walking approach [ 22 ]. With the availability of whole genome sequences for L. cuprina [ 36 ] and C. hominivorax [ 37 ], future driver strains can be made with gene promoters isolated from the species of interest.…”