Phylogeny, integration and expression of sigma virus-like genes in Drosophila

The recent and surprising discovery of widespread NIRVs (non-retroviral integrated RNA viruses) has highlighted the importance of genomic interactions between non-retroviral RNA viruses and their eukaryotic hosts. Among the viruses with integrated representatives are the rhabdoviruses, a family of negative sense single-stranded RNA viruses. We identify sigma virus-like NIRVs of Drosophila spp. that represent unique cases where NIRVs are closely related to exogenous RNA viruses in a model host organism. We have used a combination of bioinformatics and laboratory methods to explore the evolution and expression of sigma virus-like NIRVs in Drosophila. Recent integrations in Drosophila provide a promising experimental system to study functionality of NIRVs. Moreover, the genomic architecture of recent NIRVs provides an unusual evolutionary window on the integration mechanism. For example, we found that a sigma virus-like polymerase associated protein (P) gene appears to have been integrated by template switching of the blastopia-like LTR retrotransposon. The sigma virus P-like NIRV is present in multiple retroelement fused open reading frames on the X and 3R chromosomes of Drosophila yakuba - the X-linked copy is transcribed to produce an RNA product in adult flies. We present the first account of sigma virus-like NIRVs and the first example of NIRV expression in a model animal system, and therefore provide a platform for further study of the possible functions of NIRVs in animal hosts.

Highlights► Sigma virus-like genes are present in Drosophila genomes. ► The viral P mRNA was integrated via template switching by a host retrotransposon. ► The viral P integration is being expressed by the host fly, D. yakuba. ► NIRV expression in a model animal system provides a platform for functional study.