Abstract：miRNA (micoRNA) is a very important post transcriptional regulatory factor, and have been identified in many species, whereas miRNA related studies were poor in horse (Equus caballus). In this study, we carried out small RNA sequencing on mixed sample of 8 tissues of Mongolian horse with Solexa sequencing technology and analysed expression abundance of conserved and candidate miRNA, and predicted their target genes with relevant bioinformatic analysis. 5 922 735 clean reads were obtained after trimming low quality reads and adapter sequences from 9 478 925 raw reads which were generated from Illumina Miseq platform. Among them, 5 199 802 reads (15~30 nt) were selected from clean reads for subsequent analysis. After length distribution analysis, we found that total sequences were abundant in 20~24 nt that mainly based on 22 nt, which similar with length distribution of unique sequences. For small RNA annotation, total sequences distributed most in known miRNAs (69%), while unique sequences distributed most in rRNA (49%). Then we compared unique sequences with known miRNAs in miRBase and identified 239 conserved miRNAs and 243 miRNA precursors. In addition, we predicted 510 miRNAs and 375 miRNA precursors with all sequences using Mireap software, in which 238 miRNAs could be matched with horse known miRNAs and 272 non-matched miRNAs might be horse candidate novel miRNAs. The minimal folding free-energy (MFEs) of miRNA precursors reached 18.2~62.8 kcal/mol, which accordant with the requirement of its secondary structural stability. 23 037 target genes and 1 974 153 target sites for all predicted miRNAs were predicted by using miRanda software. These results enrich the horse miRNA database and can provide useful information for further related researches.
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