Genome mining shows that retroviruses are pervasively invading vertebrate genomes

Abstract

Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.

Intact genomic copies of envelope carrying retroelements are found widespread across metazoans

“…This includes species from ancient phyla such as Cnidaria, Tunicates and Ctenophora, but excludes Echinodermata and Porifera (Fig 1B). We similarly find that intact copies of env -containing vERVs are found in all vertebrate orders including jawless fish, which is consistent with previous studies 13,14 . In both cases, each element has multiple intact copies in their respective host genomes (Table S1), indicating that they have likely been actively transposing recently.…”

Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapeworm Ligula intestinalis

“…This finding is in line with the high volume of repetitive DNA in the Ligula genome, and it is further supported by our transcriptome data, which indicates that DNA integration is significantly over-represented in the larval stage of the tapeworm (electronic supplementary material, table S7). Occurrence of retrovirus genes might be a consequence of horizontal gene transfer events from its cypriniform fish hosts, which are known to have genomes significantly invaded by retrovirus genes [68]. In a similar way, virus or virus-like particles resembling RNA viruses have been observed in various parasitic groups, from protozoans to nematodes [69,70].…”

A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats

“…However, it is interesting to note that this family is less represented in wild sheep, but contrary to the domestic sheep contain several copies with intact ORFs suggesting possible differences in regulatory systems between species of the same genus. Certain copies from this family have previously been identified as potential invaders of small ruminant genomes (68,92), suggesting that this family has not been completely silenced by transposable element regulatory processes. Other studies have described this family as playing an important role in placental morphogenesis in sheep (93,94) and found expression of these copies in similar tissues in goats (95).…”