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Abstract BackgroundInsects 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. MethodsIn 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. ResultsWe 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. ConclusionOur 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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Meta-synthesis reveals interconnections among apparent drivers of insect biodiversity loss
Abstract Scientific and public interest in the global status of insects has surged recently; however, understanding the relative importance of different stressors and their interconnections remains a crucial problem. We use a meta-synthetic approach to integrate recent hypotheses about insect stressors and responses into a network containing 3385 edges and 108 nodes. The network is highly interconnected, with agricultural intensification most often identified as a root cause. Habitat-related variables are highly connected and appear to be underdiscussed relative to other stressors. We also identify biases and gaps in the recent literature, especially those generated from a focus on economically important and other popular insects, especially pollinators, at the expense of non-pollinating and less charismatic insects. In addition to serving as a case study for how meta-synthesis can map a conceptual landscape, our results identify many important gaps where future meta-analyses will offer critical insights into understanding and mitigating insect biodiversity loss.
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- PAR ID:
- 10587280
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- BioScience
- ISSN:
- 0006-3568
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/biosci/biaf034
