Brown , Katherine and Moreton , Joanna and Malla , Sunir and Aboobaker , A

The recently released draft horse genome is incompletely characterised in terms of its repetitive element profile. This paper presents a characterisation of the endogenous retrovirus (ERVs) of the horse genome based on a data-mining strategy using murine leukaemia virus proteins as queries. Nine hundred and seventy eight ERV gene sequences were identified. Sequences were identified from the gamma, epsilon and beta retrovirus genera. At least one full length gammaretroviral locus was identified, though the gammaretroviral sequences are very degenerate. Using these data the RNA expression of these ERVs were derived from a deep sequencing data set from a variety of equine tissues. Unlike the well studied human and murine ERVs there do not appear to be particular phylogenetic groups of equine ERVs that are more transcriptionally active. Using this novel approach provided a more technically feasible method to characterise ERV expression than previous studies.