An integrated mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons

Abstract

1Although mosquitoes are major transmission vectors for pathogenic arboviruses, 2 viral infection has little impact on mosquito health. This immunity is due in part to 3 mosquito RNA interference (RNAi) pathways that generate antiviral small interfering 4 RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). RNAi also maintains genome 5 integrity by potently repressing mosquito transposon activity in the germline and soma. 6 However, viral and transposon small RNA regulatory pathways have not been 7 systematically examined together in mosquitoes. Therefore, we developed an integrated 8 Mosquito Small RNA Genomics (MSRG) resource that analyzes the transposon and 9 virus small RNA profiles in mosquito cell cultures and somatic and gonadal tissues 10 across four medically important mosquito species. Our resource captures both somatic 11 and gonadal small RNA expression profiles within mosquito cell cultures, and we report 12 the evolutionary dynamics of a novel Mosquito-Conserved piRNA Cluster Locus 13 (MCpiRCL) composed of satellite DNA repeats. In the larger culicine mosquito genomes 14 we detected highly regular periodicity in piRNA biogenesis patterns coinciding with the 15

Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways

“…Interestingly, the female somatic tissues of Cu. quinquefasciatus have higher expression of transposon-mapping piRNAs, a feature not present in fruit flies [ 46 ].…”

“…Perhaps the tremendous genomic expansion in the culicine mosquitoes and greater capacity to be more prolific viral vectors compared to anopheline mosquitoes causes a biological need for culicine mosquitoes to express piRNAs in all tissues. In stark contrast to anopheline and Drosophilids, the piRNAs in culicine mosquitoes are detected in both germline and somatic cells and have similar expression levels to miRNAs ( Figure 3 A) [ 46 , 95 ]. This unique characteristic of bountiful somatic piRNAs in culicine mosquitoes prompts the question of why piRNAs are so restricted to the germline in Drosophila ?…”

“…Ultimately, the transcriptional control of piRNA expression may be exceptionally narrow in Drosophila , as only four out of many tens of known Drosophila cell lines display robust piRNA expression (FGS, OSS/OSC, WRR1, Kc167) [ 102 , 103 , 104 , 105 , 106 ]. In contrast, every mosquito cell line we have analyzed expresses robust piRNAs [ 46 ] and many other lepidopteran insect cells also express abundant piRNAs [ 107 , 108 , 109 , 110 ]. In fact, the physiologically broader expression of piRNAs in mosquito somatic cells is a common trend in most other insect species [ 47 ].…”

“…aegypti discussed a mosquito piRNA cluster analogous to the Drosophila flamenco cluster [ 137 ], but we believe greater insight into mosquito piRNA cluster evolution is gained through multiple-species comparisons that include piRNAs from Cu. quinquefasciatus [ 46 , 96 ].…”

“…Although animal small RNA classes are technically defined/annotated by criteria different from originating locus and protein they are bound to [ 45 ], read length and sequence matching to existing databases can serve as an approximate proxy of the proportions of these small RNA classes ( Figure 1 B). For example, we observed varying proportions of miRNAs, endo-siRNAs, and piRNAs that form distinct profiles between Drosophilids and Culicidae [ 46 ]. These distinct small RNA class profiles may reflect the specific genomic, physiological, and evolutionary divergence between Drosophilids and Culicidae.…”