Abstract
Endogenous retroviruses (ERVs) are the remnants of past retroviral infections that once invaded the host’s germline and were vertically transmitted. ERV sequences have been reported in mammals, but their distribution and diversity in cervids are unclear. Using next-generation sequencing, we identified a nearly complete genome of an endogenous betaretrovirus in fallow deer (Dama dama). Further genomic analysis showed that this provirus, tentatively named cervid endogenous betaretrovirus 1 (CERV β1), has typical betaretroviral genome features (gag-pro-pol-env) and the betaretrovirus-specific dUTPase domain. In addition, CERV β1 pol sequences were detected by PCR in the six non-native deer species with wild populations in Australia. Phylogenetic analyses demonstrated that CERV β1 sequences from subfamily Cervinae clustered as sister taxa to ERV-like sequences in species of subfamily Muntiacinae. These findings, therefore, suggest that CERV β1 endogenisation occurred after the split of these two subfamilies (between 3.3 and 5 million years ago). Our results provide important insights into the evolution of betaretroviruses in cervids.
Highlights
Endogenous retroviruses (ERVs) represent remnants of past retrovirus infections, which became integrated into the host germline and were passed to progeny cells; and can comprise up to 10% of vertebrate genomes [1,2]
As part of a pathogen search in Australian wild deer [23], Genomic DNA (gDNA) extracted from blood specimens collected in four fallow deer were subjected to next-generation sequencing
After trimming and host-genome removing, a total of 22,814,671 PE reads were retained. These datasets were searched for possible pathogen-derived sequences, and here we focus on reporting the presence of apparent endogenous retrovirus-like sequences, displaying the closest relatedness with betaretroviruses identified in goats (Table 1)
Summary
Endogenous retroviruses (ERVs) represent remnants of past retrovirus infections, which became integrated into the host germline and were passed to progeny cells; and can comprise up to 10% of vertebrate genomes [1,2]. Some ERVs are transcriptionally active and have maintained intact open reading frames for some of their genes [3], suggesting that these elements may benefit their hosts, possibly protecting against exogenous retrovirus infection [4]. In contrast to classes I and III, the class II ERVs have a more restricted host range, comprised mainly of mammals and birds; they have recently been detected in amphibians [6,7,8]. Betaretrovirus-related elements have been previously detected in wild cervid genomes such as caribou (Rangifer tarandus) and white-tailed deer (Odocoileus virginianus) utilising PCR assays targeting conserved regions of the retroviral pro and/or pol genes; these elements still remain uncharacterised [6]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
