Characterization of the Barley (Hordeum vulgare L.) miRNome: A Computational-Based Update on MicroRNAs and Their Targets

MicroRNAs (miRNAs) are a class of endogenous noncoding small RNAs acting on gene regulation at posttranscriptional level, a phenomenon known in plants as posttranscriptional gene silencing. miRNAs are known to play key regulatory roles in plant response to stress, besides being involved in development and morphogenesis. To extend and to update information on miRNAs and their targets in barley and to identify candidate polymorphisms at miRNA target sites, the features of previously known plant miRNAs have been used to systematically search for barley miRNA homologues and targets in the publicly available EST database. Matching sequences have then been related to UniGene clusters on which most of this study was based. One hundred fifty-six microRNA mature sequences belonging to 50 miRNA families have been found to significantly match at least one EST sequence in barley. The predicted miRNA targets were ascribed to different pathways, among others the response to abiotic stress. To verify experimentally the barley miRNAs and their involvement in stress response, the barley miRNome of plants exposed to low temperatures has been characterized by a deep sequencing approach on Illumina GAIIx. Many of the known miRNAs have been found as different isomeric variants, so-called isomiRs, which might increase the target repertoire of the miRNA gene they derive from.