MicroRNAs (miRNAs) are evolutionarily conserved small non-coding RNAs that regulate gene expression. In livestock species, miRNAs also show great potential as biomarkers for animal health and product quality. In sheep, few miRNAs have been described in comparison with other livestock species or model organisms. We uniformly analyzed 172 public ovine small RNA sequencing datasets from 21 different tissues in order to predict conserved and novel miRNA precursors and profile their expression patterns. In addition to the 106 annotated sheep miRNAs, 1047 previously unannotated miRNA precursor sequences were detected and 41 % of them were assigned an orthologue from other close species. Considering expression levels, a set of miRNAs with high sequence conservation were detected in all tissues, while 733 mature miRNAs were robustly expressed in at least one tissue. 270 miRNAs showed high tissue specificity index values. Brain, male reproductive tissues and PBMCs showed the most distinct expression patterns. Strikingly, over one hundred precursors from the ruminant specific family of mir-2284/mir-2285 miRNAs were found, which were enriched in immune related tissues. This work supports the known high conservation of many miRNAs, but also highlights the potential of clade-specific innovations in ruminant evolution.
