Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing

The recently released draft horse genome is incompletely characterised in terms of its repetitiveelement profile. This paper presents characterisation of the endogenous retrovirus (ERVs) of the horsegenome based on a data-mining strategy using murine leukaemia virus proteins as queries. 978 ERVgene sequences were identified. Sequences were identified from the gamma, epsilon and betaretrovirusgenera. At least one full length gammaretroviral locus was identified, though the gammaretroviralsequences are very degenerate. Using these data the RNA expression of these ERVs were derived fromRNA transcriptome data from a variety of equine tissues. Unlike the well studied human and murineERVs there do not appear to be particular phylogenetic groups of equine ERVs that are moretranscriptionally active. Using this novel approach provided a more technically feasible method tocharacterise ERV expression than previous studies