Untangling aphids virome from its endogenous viral elements

The potato aphid, Macrosiphum euphorbiae,  is an important cosmopolitan agricultural pest and a vector of multiple plant viruses. This species is also a host of several insect-specific viruses and endosymbiotic bacteria. Despite M. euphorbiae's economic importance, there are few genomic resources available. We used RNAseq and DNAseq to characterize the virome of these aphids in East Tennessee. Our data identified several insect-specific viruses, plant viruses, and phages infecting endosymbiotic bacteria. More importantly, we found that a previously described ‘Ambidensovirus’ is an actual homolog of an endogenous viral element that may play a role in plastic wing formation. Our study highlights how a combination of RNA and DNA can be necessary to overcome the potential pitfalls of RNAseq-only viral discovery viromes. We emphasize the need for careful analysis of RNAseq data for insect viral discovery.