Assessing the Diversity of Endogenous Viruses Throughout Ant Genomes

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.

Keywords: Formicidae; comparative genome biology; endogenous viral elements; microbes; viral diversity.

FIGURE 1

Phylogeny of ants with sequenced genomes used in this study colored by subfamily (left), ant genome size in mb (middle), and number of EVE hits per genome (right). Ant EVE hit numbers are colored by viral protein to which they were found to be most similar in the blastx analysis.

FIGURE 2

(A) Glycoprotein Mono-Chu Phylogeny. The phylogeny was obtained from maximum likelihood analysis of the glycoprotein multiple amino acid alignment, including both ant EVE sequences and closely related exogenous viruses. The best fit protein substitution model was JTT + G + F. ML non-parametric bootstrap values >70 (1000 replicates) are indicated at each node. Scale bar indicates evolutionary distance in substitutions per site. The 224 ant EVEs which comprise their own clade have been collapsed and are represented by the red triangle. The tips are colored by associated host. The gray bars on the right are based on distinct clades of EVE hits. (B) Expanded phylogeny representing the clade of 224 ant EVEs which was collapsed in panel (A). ML non-parametric bootstrap values >70 (1000 replicates) are indicated at each node. Scale bar indicates evolutionary distance in substitutions per site. The gray bars on the right are based on distinct clades of EVE hits.

FIGURE 3

Tanglegram with ant phylogeny on left and glycoprotein Mono-Chu viral phylogeny on right. The exogenous viruses included in the viral phylogeny were left out because their hosts are not included in the ant phylogeny. Colors of the association are randomly prescribed for each of the ant species.