Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys.

Xiao Wang,Boshi Wang,Huijuan Pan,Zhijin Liu,Paul A. Garber

doi:10.7717/peerj.6602

Abstract

BackgroundEndogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China.MethodsWe used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences.ResultsWe identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host.ConclusionsOur results indicate that ERV sequences are widely distributed in snub-nosed monkeys, and their phylogenetic history can mirror that of their hosts over long evolutionary time scales. In addition, ERV sequences appear to have an important influence on the evolution of host pathology.

Highlights

Endogenous retroviruses (ERVs) are remnants of ancient retrovirus infections that have entered a species germ line and can be transmitted vertically to that host’s offspring (Wu et al, 2016)
Consistent with the consensus nomenclature used for the human endogenous retrovirus (HERV) (Boeke & Stoye, 1997) and the chimpanzee endogenous retrovirus (CERV) (Polavarapu, Bowen & Mcdonald, 2006), here we refer to the golden snub-nosed monkey endogenous retrovirus by the acronym GERV and black and white snub-nosed monkey endogenous retrovirus by the acronym BERV
Using the procedure described above, we identified a total of 284 GERVs with an average length of 8229 base-pairs and 263 BERVs with an average length of 8068 base-pairs (Files S3 and S4)

Summary

Introduction

Endogenous retroviruses (ERVs) are remnants of ancient retrovirus infections that have entered a species germ line and can be transmitted vertically to that host’s offspring (Wu et al, 2016). These sequences, have been detected in all vertebrates genomes including humans, and they often occupy a intermediate fraction of the genome (Blikstad et al, 2008; Gifford & Tristem, 2003). We examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. ERV sequences appear to have an important influence on the evolution of host pathology

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