Endogenous viral elements integrated into the genome of the soybean aphid, Aphis glycines

Authors: LIU, SIJUN - Iowa State University; Coates, Brad; BONNING, BRYONY - University Of Florida

Submitted to: Insect Biochemistry and Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2020
Publication Date: 6/11/2020
Citation: Liu, S., Coates, B.S., Bonning, B.C. 2020. Endogenous viral elements integrated into the genome of the soybean aphid, Aphis glycines. Insect Biochemistry and Molecular Biology. 123. Article 103405. https://doi.org/10.1016/j.ibmb.2020.103405.
DOI: https://doi.org/10.1016/j.ibmb.2020.103405

Interpretive Summary: Aphids feeding on cultivated crops reduce yield and farmer profit in the U.S. and worldwide. The emergence of resistance to chemical insecticides and tolerant host plants makes control of aphids challenging. How aphids are able to evade control practices remains largely unknown, but integration of non-insect DNA into insect genes can lead to resistance in other insect species. An ARS scientist and university researchers scanned the genome sequences of two aphid species to identify for foreign DNA. The team discovered a specific class of viruses within the soybean aphid and sugar cane aphid genomes. While present in both genomes, the virus genes appeared nonfunctional and viral DNA had not inserted within aphid genes. Since these virus DNA insertions were non-functional and were not associated with any aphid genes, it suggests they may not be a factor in the evolution of insecticide resistance. These results will be of interest to university, industry, regulatory, and government stakeholders interested in insect evolution and the mechanisms insects use to evade different control tactics.

Technical Abstract: Sequence analysis of the genomic DNA isolated from four biotypes of the soybean aphid, Aphis glycines (AG), revealed that in addition to the commonly observed retrovirus-related retrotransposons, viral sequences derived from multiple RNA and DNA viruses have integrated into the genome. Notably, sequences of more than 60 nudiviral genes were identified from de novo assembled DNA contigs, and mapped to assembled genomic scaffolds of AG, indicating an ancient nudivirus, named Aphis glycines endogenous nudivirus (AgENV), had integrated into the AG genome. Furthermore, sequences derived from a similar endogenous nudivirus, Melanaphis sacchari endogenous nudivirus (MsENV), were identified from the genomic scaffolds of the sugarcane aphid, Melanaphis sacchari. Analysis of transcriptome and small RNA sequence data derived from AG did not provide evidence for transcription of the integrated AgENV genes. Hence, the genes of AgENV may be present as pseudogenes. Phylogenetic analysis based on nudivirus core genes indicated that these aphid ENVs belong to the genus Alphanudivirus.