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This content will become publicly available on October 24, 2024

Title: Untangling an insect’s virome from its endogenous viral elements
Abstract Background

Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery.


In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphidMacrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly forM. euphorbiaeusing Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome.


We found reads from two insect-specific viruses (aFlavivirusand anAmbidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the ‘virome’ of this insect can be attributed to EVEs in the host genome.


Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.

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Award ID(s):
2305653 2152954
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
BMC SpringerNature
Date Published:
Journal Name:
BMC Genomics
Medium: X
Sponsoring Org:
National Science Foundation
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