An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes

Abstract

MicroRNA (miRNA) is a pivotal type of noncoding RNA gene in posttranscriptional gene regulation (David 2004). The majority of miRNAs in pig (Sus scrofa), an important domestic animal, remain unknown. From this perspective, we attempted the genomewide identification of novel porcine miRNAs. Here, we propose a novel integrative bioinformatics pipeline to identify conservative and nonconservative novel miRNAs. We used methods such as homology searching against known metazoan miRNAs, conservation filtering, and ab initio approaches. As a result, 222 new porcine miRNAs were identified and 14 more porcine miRNA gene families were discovered. miRNA:target pairs, 78,060, between 224 miRNAs and 4384 mRNAs have been predicted, and these miRNA targets were involved in a wide spectrum of regulatory functions and metabolic biological processes. An overall analysis of genome-scale gene locations and sequence characteristics was also conducted, and a detailed user manual of the pipeline is provided. Through this study, the number of identified porcine miRNAs increased, and an effective alternative strategy for genomewide miRNA identification was developed.