Abstract
Simian endogenous retrovirus, SERV, is a successful germ line invader restricted to Old World monkey (OWM) species. (1) Background: The availability of high-quality primate genomes warrants a study of the characteristics, evolution, and distribution of SERV proviruses. (2) Methods: Cercopithecinae OWM genomes from public databases were queried for the presence of full-length SERV proviruses. A dataset of 81 Cer-SERV genomes was generated and analyzed. (3) Results: Full-length Cer-SERV proviruses were mainly found in terrestrial OWM, and less so in arboreal, forest- dwelling monkeys. Phylogenetic analysis confirmed the existence of two genotypes, Cer-SERV-1 and Cer-SERV-2, with Cer-SERV-1 showing evidence of recent germ-line expansions. Long Terminal Repeat (LTR) variation indicated that most proviruses were of a similar age and were estimated to be between <0.3 and 10 million years old. Integrations shared between species were relatively rare. Sequence analysis further showed extensive CpG methylation-associated mutations, variable Primer Binding Site (PBS) use with Cer-SERV-1 using PBSlys3 and Cer-SERV-2 using PBSlys1,2, and the recent gain of LTR motifs for transcription factors active during embryogenesis in Cer-SERV-1. (4) Conclusions: sequence analysis of 81 SERV proviruses from Cercopithecinae OWM genomes provides evidence for the adaptation of this retrovirus to germ line reproduction.
Highlights
Mobile genetic elements, including viruses, abound in living organisms
It has been firmly recognized that Endogenous Viral Elements (EVEs) are derived from viruses that were once infectious; endogenization of exogenous retroviruses can be seen in action in several species, for instance, murine leukemia virus (MLV) in mice, feline leukemia virus in cats, and koala retrovirus in koalas
Sequences homologous to Cer-Simian Endogenous Retrovirus (SERV) were retrieved from all analyzed Old World monkey (OWM) genomes, but full-length proviral insertions with >90% homology to the query sequence were restricted to C. sabaeus, E. patas, M. leucophaeus, P. anubis, T. gelada, and the Asian macaque species M. fascicularis, M. fuscata, M. mulatta, and M. nemestrina (Table 1)
Summary
Mobile genetic elements, including viruses, abound in living organisms. They add considerably to the flexibility and gene content of both pro- and eukaryotic genomes. After deleterious insertions from the germ line were purged, many of the Endogenous Viral Elements (EVEs) left behind have mutated over time and some have been adopted by the host. Such processes are of great value when studying the reshaping of genomes, but an often forgotten aspect of EVEs is the information that captured viral sequences can give us about the deep history of the viruses themselves. A related virus, simian D type retrovirus (SRV), is at present infectious and pathogenic in macaques [5]
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