Assessing the Diversity of Endogenous Viruses Throughout Ant Genomes.

Peter J Flynn,Corrie S Moreau

doi:10.3389/fmicb.2019.01139

Peter J Flynn, Corrie S Moreau

Open Access

https://doi.org/10.3389/fmicb.2019.01139

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Abstract

Endogenous viral elements (EVEs) can play a significant role in the evolution of their hosts and have been identified in animals, plants, and fungi. Additionally, EVEs potentially provide an important snapshot of the evolutionary frequency of viral infection. The purpose of this study is to take a comparative host-centered approach to EVE discovery in ant genomes to better understand the relationship of EVEs to their ant hosts. Using a comprehensive bioinformatic pipeline, we screened all nineteen published ant genomes for EVEs. Once the EVEs were identified, we assessed their phylogenetic relationships to other closely related exogenous viruses. A diverse group of EVEs were discovered in all screened ant host genomes and in many cases are similar to previously identified exogenous viruses. EVEs similar to ssRNA viral proteins are the most common viral lineage throughout the ant hosts, which is potentially due to more chronic infection or more effective endogenization of certain ssRNA viruses in ants. In addition, both EVEs similar to viral glycoproteins and retrovirus-derived proteins are also abundant throughout ant genomes, suggesting their tendency to endogenize. Several of these newly discovered EVEs are found to be potentially functional within the genome. The discovery and analysis of EVEs is essential in beginning to understand viral–ant interactions over evolutionary time.

Highlights

Endogenous viral elements (EVEs), or viral fossils, are whole or fragmented viral sequences integrated into host genomes after viral infection, which can propagate through the germline
Around half of the EVEs we found across the ant genomes included nonsense mutations from premature stop codons
Discovered EVEs were found within all ant genomes and are similar to a large diversity of viral lineages

Summary

Introduction

Endogenous viral elements (EVEs), or viral fossils, are whole or fragmented viral sequences integrated into host genomes after viral infection, which can propagate through the germline. The majority of research conducted on endogenous viruses centers around retroviruses, which has led to discoveries demonstrating that these viruses could play a role in the evolution of their hosts. Endogenous viral elements are created when a duplicate of a double-stranded DNA viral genome is incorporated into the host germline. As part of their replication, retroviruses must manufacture dsDNA intermediates in order to integrate into the host genome.

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