Expression and evolutionary analysis of microRNAs in Cochliomyia hominivorax and Cochliomyia macellaria: Implications for parasitism studies in Calliphoridae (Diptera: Brachycera)

MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional modulators of gene expression in Eukaryotes. The imperfect complementarity between miRNAs and the 3’ untranslated region of mRNAs inhibits their translation in animals, being key genes for control of expression in cells. The characterization of miRNAs provides a better understanding of biological processes and evolution of traits in different species. The family Calliphoridae is a group of myiasis-causing flies with different feeding habits, including the species Cochliomyia hominivorax (screwworm fly) and Cochliomyia macellaria (secondary screwworm). The screwworm fly is one of the major pests in Neotropical region. Their larvae infest and feed on live tissues of warm-blooded vertebrates, resulting in severe losses for livestock industry. Differently, the close-related secondary screwworm shows a saprophagous habit, feeding on carcasses and dead tissues, being crucial for forensic entomology and public health. Because of their close evolutionary relationship and contrasting feeding habits, they are ideal models to study the molecular basis of parasitism and feeding specialization in the family Calliphoridae and, therefore, in order Diptera. To characterize the miRNAs of both species, the small-RNA transcriptomes of adults (male and female) and larvae (third instar) were sequenced using Illumina MiSeq next generation sequencing platform. The 6.2 million reads generated were mapped against the Drosophila melanogaster genome and screened in miRBase. We identified 69 miRNAs in C. hominivorax and 71 in C. macellaria, conserved since the Nephrozoa ancestor (641 MYA) in the basis of Bilaterian clade. Nucleotide substitutions were biased to 3’-end portion of the miRNAs with rare seed region shifting. The preliminary expression profile revealed 43 differentially expressed miRNAs between species, gender and life stages, given by hierarchical clustering analysis. These results will provide new information about the genetic background of parasitic habits in Calliphoridae, with prospects to evolutionary studies in Diptera and pest-management control.