The virome of Drosophila suzukii, an invasive pest of soft fruit

Abstract

Drosophila suzukii (Matsumura) is one of the most damaging and costly pests to invade temperate horticultural regions in recent history. Conventional control of this pest is challenging, and an environmentally benign microbial biopesticide is highly desirable. A thorough exploration of the pathogens infecting this pest is not only the first step on the road to the development of an effective biopesticide, but also provides a valuable comparative dataset for the study of viruses in the model family Drosophilidae. Here we use a metatransciptomic approach to identify viruses infecting this fly in both its native (Japanese) and invasive (British and French) ranges. We describe eighteen new RNA viruses, including members of the Picornavirales, Mononegavirales, Bunyavirales, Chuviruses, Nodaviridae, Tombusviridae, Reoviridae, and Nidovirales, and discuss their phylogenetic relationships with previously known viruses. We also detect 18 previously described viruses of other Drosophila species that appear to be associated with D. suzukii in the wild.

Endogenization from diverse viral ancestors is common and widespread in parasitoid wasps

“…A custom database was made to identify contigs that contain genes of viral origin and exclude contaminant contigs (Medd et al 2018) . The database contained all protein sequences from the NCBI refseq database (downloaded February 2019) from Hymenoptera, Lepidoptera, Diptera, Coleoptera, bacteria, archaea, nematodes, and fungi, and viral protein sequences from the NCBI nr database (downloaded February 2019).…”

“…Exhaustive screening of ORFs for viral hits. The first approach used was modified from Medd et al 2018, and used exhaustive similarity searches of all possible Open Reading Frames (ORFs) (of a minimum size) against a curated database to identify sequences with similarity to viral proteins. Despite the fragmented state of the newly added genome assemblies, it was reasoned that the majority of genes of viral origin and architecture would be intact (not be broken into pieces across contigs) because N50 values were equal to or greater than the expected sizes of these genes (less than 1000 base pairs on average).…”

A new lineage of segmented RNA viruses infecting animals

“…Excel table giving the number of positive and negative sense forward-reads for each segment of Nete virus, with comparison ratios for high abundance viruses reported in Waldron et al (2018) and Medd et al (2018)…”

Expansion of the metazoan virosphere: progress, pitfalls, and prospects

“…First, the nature and quantity of the nucleic acid provides useful clues. Endogenous DNA copies can be identified by a comparison of PCR and RT-PCR (or direct DNA and RNA sequencing) [10,11,13,48]. For example, functional DNA viruses must express their proteins, so that the absence of viral mRNAs argues against active replication.…”

“…For example, functional DNA viruses must express their proteins, so that the absence of viral mRNAs argues against active replication. Active replication also affects strand-bias in RNA viruses, so that strand-specific PCR [49] or RNA sequencing can identify the negative-sense replication intermediates of positive-sense single-stranded (+ss) RNA viruses, and quantitative analyses can detect the presence of coding products from -ssRNA and dsRNA viruses [48]. And, for both DNA and RNA viruses, contaminating sequences are likely to be at relatively low titre, whereas the copy-number of inherited EVEs will match the host genome.…”