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

Maxwell J Scott,Samuel T Bailey,Ellen O Martinson,Gladys Quintero,Gisele A Cardoso,Mario Vasquez,Virag Varga,Agustin Sagel,Steven R Skoda,Adam M Phillippy,Tatiana T Torres,Joshua B Benoit,Matthew T Weirauch,Paul V Hickner,Zainulabeuddin Syed,Rebecca J Davis,Elizabeth H Scholl

doi:10.1038/s42003-020-01152-4

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.

Highlights

The New World Screwworm fly, Cochliomyia hominivorax, is a major pest of livestock in South America and Caribbean
We identified 78 canonical olfactory receptors (ORs) plus the olfactory receptor co-receptor (Orco) in the C. hominivorax genome, which is similar in number to M. domestica and S. calcitrans (Table 2, Supplementary Data 4, and Supplementary Fig. 1)
The whole-genome assembly of the New World screwworm reported in this study will serve as a reference for future genetic investigations of this obligate parasite of warm-blooded animals

Summary

Introduction

The New World Screwworm fly, Cochliomyia hominivorax, is a major pest of livestock in South America and Caribbean. 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). For suppression of the targeted pest population, the TESS would be mass-reared and males released at regular intervals in excess of the wild population As such a program could be costly, several alternative genetic strategies are under development that potentially could be more efficient and less expensive[8]. In addition to identifying suitable target genes, building gene drive strains requires identification of suitable gene promoters for driving Cas[9] expression in the germline and for expression of gRNAs. A better understanding of C. hominivorax development and behavior would facilitate genetic control programs. A complete repertoire of chemosensory genes could allow for the identification of more effective chemical control

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Conclusion