The discovery, distribution and diversity of DNA viruses associated withDrosophila melanogasterin Europe

Abstract

Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described in association with the Drosophilidae. This has limited the opportunity to use natural host-pathogen combinations in experimental studies, and may have biased our understanding of the Drosophila virome. Here we describe fourteen DNA viruses detectable by metagenomic analysis of 6.5 thousand pool-sequenced Drosophila, sampled from 47 European locations between 2014 and 2016. These include three new Nudiviruses, a new and divergent Entomopox virus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of Galbut virus, an RNA Partitivirus, segregating at very low frequency. Remarkably, we show that Vesanto virus, a small DNA virus previously described as a Bidnavirus, may be composed of up to 12 segments and represents a new lineage of segmented DNA viruses. Only two of the DNA viruses, Kallithea virus (Nudiviridae) and Vesanto virus (Bidna-virus like) are common, being found in 2% or more of wild flies. The other viruses are rare, with many likely to be represented by a single infected fly in the collection. We find that virus prevalence in Europe reflects that seen in publicly-available datasets, with Kallithea virus and Vesanto virus being commonly detectable in data from wild-caught flies and large population cages, and the others being rare or absent. These analyses suggest that DNA viruses are generally rarer than RNA viruses in D. melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redress the earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.

Genomic analysis reveals an exogenous viral symbiont with dual functionality in parasitoid wasps and their hosts

“…A partial poxvirus genome sequence identified within the argentine ant, named Linepithema humile entomopoxvirus 1 (LHEV), represents the first hymenopteran (ant, wasp, and bee) poxvirus to be sequenced [ 43 ]. In addition, a complete poxvirus genome obtained from Drosophila melanogaster , known as Yalta virus, represents the first sequenced dipteran (fly) poxvirus [ 44 ].…”

“…The placement of the 7 originally sequenced EPVs (MSEV, AMEV, AHEV, MySEV, CREV, CBEV, and ACEV) on the tree shows concordance with the higher phylogenetic relationships of their insect hosts, which is consistent with previous EPV phylogenetic analyses [ 37 , 40 ]. In contrast, LHEV and Yalta virus show a clear divergence from other EPVs [ 44 ]. The inclusion of DlEPV in our phylogeny revealed that it shares a more recent common ancestor with Yalta virus than LHEV, suggesting that DlEPV is more likely derived from a fly pathogen rather than a parasitoid pathogen ( Fig 2 ).…”

“…We determined that 44 of the 49 poxvirus core genes are shared between the DlEPV and Yalta virus genomes ( S3 Table ). Interestingly, 2 of the 3 “missing” genes in the Yalta virus genome were also not detected in the DlEPV genome [ 44 ]. This suggests that the absence, or more likely, extreme sequence divergence of these genes is lineage-specific to fly poxviruses, rather than due to genome incompleteness.…”

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

“…Sequences were re-aligned in the proximity of insertions-deletions (indels) with GATK (v3.4-46; McKenna et al 2010). We identified and removed any reads that mapped to the D. simulans genome using a custom python script, following methods outlined previously (Machado et al 2019; Kapun et al 2020; for a more in-depth analysis of D. simulans contamination see Wallace et al 2020).…”

“…Sequences were re-aligned in the proximity of insertions-deletions (indels) with GATK (v3.4-46;McKenna et al 2010). We identified and removed any reads that mapped to the D. simulans genome using a custom python script, following methods outlined previously (Kapun et al 2020;Machado et al 2021; for a more in-depth analysis of D. simulans contamination see Wallace et al 2021). Although this method of decontamination by D. simulans accurately estimates contamination rate and removes the vast majority of D. simulans reads (Machado et al 2021), care should be taken when analyzing samples with higher contamination rates at sites that are shared polymorphisms between the two species.…”