microRNA Expression Dynamics in Culicoides sonorensis Biting Midges Following Blood-Feeding

SIMPLE SUMMARY: Culicoides sonorensis midges are able to transmit pathogenic viruses to livestock, resulting in significant economic losses. Virus transmission is linked to blood feeding, where female C. sonorensis midges require blood to produce eggs. Due to the relationship between egg development, blood feeding, and pathogen transmission, there is a need to understand midge physiology to control virus transmission. One aspect of midge physiology that has yet to be explored is microRNAs (miRNAs), which display different expression patterns related to egg development and pathogen infection. miRNAs degrade messenger RNAs in a sequence-specific manner which stops associated protein production. To determine the Culicoides miRNA catalog, we sequenced small RNA molecules (small RNA-Seq) and used bioinformatic analyses (miRDeep2) of whole female midges and digestive tissues before and after blood feeding. Our analyses characterized 76 miRNAs within C. sonorensis. Based on our findings, we suggest an interesting evolutionary relationship between miRNA expression and blood meal requirements across blood-feeding insects. We also identified miRNAs with expression patterns regulated by blood meal ingestion and/or tissue. Lastly, we identified potential miRNAs regulated by virus infection. Overall, our data provide a foundation for future studies to determine the mechanisms of gene regulation associated with midge physiology and virus transmission. ABSTRACT: Culicoides sonorensis midges vector multiple livestock arboviruses, resulting in significant economic losses worldwide. Due to the tight association between virus transmission, blood feeding, and egg development, understanding midge physiology is paramount to limiting pathogen transmission. Previous studies have demonstrated the importance of small non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs), in multiple aspects of vector physiology. These small ncRNAs regulate gene expression at the post-transcriptional level and display differential expression during pathogen infection. Due to the lack of annotated miRNAs in the biting midge and associated expression profiles, we used small RNA-Seq and miRDeep2 analyses to determine the Culicoides miRNAs in whole females and midgut tissues in response to blood feeding. Our analyses revealed 76 miRNAs within C. sonorensis composed of 73 orthologous and three candidate novel miRNAs, as well as conserved miRNA clusters. miRNA conservation suggests an interesting evolutionary relationship between miRNA expression and hematophagy in the infraorder Culicomorpha. We also identified multiple blood meal-regulated and tissue-enriched miRNAs. Lastly, we further identified miRNAs with expression patterns potentially associated with virus infection by probing publicly available datasets. Together, our data provide a foundation for future ncRNA work to untangle the dynamics of gene regulation associated with midge physiology.