Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co‐opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a nonretroviral RNA virus (nrEVE) was shown to produce PIWI‐interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence‐specific mechanism for antiviral immunity, analogous to piRNA‐mediated silencing of transposable elements. Here, we combine population genomics and evolutionary approaches to analyse the genomic architecture of nrEVEs in A. aegypti. We conducted a genome‐wide screen for adaptive nrEVEs and searched for novel population‐specific nrEVEs in the genomes of 80 individual wild‐caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental‐dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex with only a few nrEVEs contributing to adaptive evolution in A. aegypti.

中文翻译：

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虫媒病毒载体埃及伊蚊的群体基因组学揭示了内源病毒元件的基因组结构和进化

从病毒到真核细胞的水平基因转移是一种普遍现象。体细胞病毒整合与持续性病毒感染有关，而与种系细胞的整合则通过垂直传播维持在宿主基因组中，并且可能被宿主功能所利用。在虫媒病毒载体埃及伊蚊中，来自非逆转录病毒 RNA 病毒 (nrEVE) 的内源病毒元件被证明可以产生 PIWI 相互作用 RNA (piRNA)，以限制同源病毒的感染。因此，nrEVEs可能构成一种可遗传的、序列特异性的抗病毒免疫机制，类似于piRNA介导的转座元件沉默。在这里，我们结合群体基因组学和进化方法来分析埃及伊蚊中 nrEVE 的基因组结构。我们对适应性 nrEVE 进行了全基因组筛选，并在来自 5 个地理种群的 80 只野生捕获蚊子的基因组中寻找新的种群特异性 nrEVE。我们展示了蚊子基因组中 nrEVE 的动态景观，并鉴定了源自两种当前流行病毒的五种新型 nrEVE，为 piRNA 簇的环境依赖性修饰提供了证据。总的来说，我们的结果表明病毒内源化事件很复杂，只有少数 nrEVE 对埃及伊蚊的适应性进化做出了贡献。