In the model organism Drosophila melanogaster, the PIWI-interacing RNA pathway contributes in silencing transposable elements (TEs) through smallRNAs (piRNAs), which arise from genomic loci (piRNA clusters) that contain sequences of previously-acquired TEs. As such, they are a functionally-immune archive of previous TE invasions that is passed to the offspring. In the arboviral vector Aedes aegypti, piRNA clusters contain TEs and endogenous viral elements from nonretroviral RNA viruses (nrEVEs) which produce piRNAs, supporting the hypothesis that nrEVEs are heritable immunity effectors. However, direct evidence that nrEVEs mediate adaptive immunity is lacking. Here, by using an analytic approach intersecting population genomics with molecular biology we demonstrate that the composition of piRNA clusters is modular through acquisition and absence of nrEVEs. We show that the genomes of wild-caught mosquitoes have a different set of nrEVEs than those annotated in the reference genome, including population-specific integrations. nrEVEs are not distributed in mosquito genomes only by genetic drift, but some show signs of positive selection. Moreover, by comparing natural mosquito populations expressing or lacking two newly characterised nrEVEs with high sequence complementarity to cell fusing agent virus, we show that nrEVEs confer antiviral immunity in ovaries against the cognate virus. Our results confirm that some nrEVEs have been co-opted for adaptive immunity to viral infections.

Immunity to infections in arboviral vectors by integrated viral sequences: an evolutionary perspective