Identification of Novel Endogenous Retroviruses in Anura

Abstract

Endogenous retroviruses (ERVs) represent remnants of past retroviral infections and have had a pivotal role in vertebrate evolution, contributing toward the generation of novel genes and regulatory elements. The majority of ERV research to date has had a mammalian focus; Anurans (the order of amphibians consisting of frogs and toads) are comparable in genome size and number of extant species and yet very few ERVs have been described in this order. Under the current classification, alpharetroviruses appear to be avian-specific; here we screened 47 publicly available Anuran genomes for alpharetroviruses using a bioinformatic pipeline. Both truncated and full-length ERV elements were identified through this screening process which were represented by multiple loci. Ten families of novel Anuran ERVs (AnERV1-10) with intact viral genes were identified in 11 anuran species, some of which are shared between multiple species. Furthermore, based on conserved domain and phylogenetic analysis, all ten novel ERV families appeared in recombined states. This included two families with alpharetrovirus classified Env proteins, although the majority had epsilonretrovirus classified Pol and gammaretrovirus classified Env proteins. These findings extend the pattern of recombination presented in two other Anuran ERVs and adds to the complex evolutionary history of retroviruses. These results suggest that analysis of other vertebrate groups beyond the mammals would provide new information on the presence and state of ERVs, providing further evidence of the modes of ERV evolution within host genomes and their role in the diversification of the vertebrate tree of life.