Endogenous viral elements (EVEs) are genomic remnants of ancient viruses integrated into host DNA, and are present in every vertebrate. EVEs arise during active viral infection and, if integrated in germline cells, can be passed on through progeny and become fixated in a population over time. EVEs provide a valuable record of past infections and coevolution of viruses and hosts over millions of years.
Genoviromes, or the total EVEs in a genome, are a unique way of identifying viruses capable of infecting a species without the need to isolate the virus during infection. EVEs have been implicated in RNA antiviral defence through mechanisms similar to CRISPR in bacteria. Investigating the genovirome of a species helps in understanding the mechanism of EVE selection in host genomes and previous infections the species has faced.
This study aimed to characterise the genovirome of the Tasmanian devil; an endangered marsupial restricted to the island of Tasmania. We used a BLAST-based bioinformatic approach to characterise the number, distribution and phylogenetics of EVEs within the genome of the Tasmanian devil. Briefly, we identified genomic regions with identity to viral genes, annotated the gene arrangement of each putative integration and highlighted conserved enzymatic motifs. We identified endogenous fragments from four viral families; ~13,000 retrovirus integrations, ~800 filovirus integrations, 13 bornavirus integrations and 16 parvoviruses integrations.
We show that Tasmanian devil endogenous retroviruses are primarily related to Betaretrovirus and Gammaretrovirus exogenous retroviruses, however many formed an EVE-specific clade. These EVE-specific retroviruses likely represent extinct lineages of retroviruses that infected Australian marsupials after the divergence from Gondwana. Tasmanian devil filovirus, parvovirus and bornavirus EVEs also form phylogenetic clades separate from known exogenous viruses, revealing an undiscovered or extinct diversity of marsupial viruses.
This study provides a comprehensive overview of the Tasmanian devil genovirome to facilitate future studies on virus evolution, EVE transcription and expression and may assist in predicting predisposition to certain diseases, or vulnerability to viral infection.