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The identification of eighteen precursor miRNA clusters and their targets in barley (Hordeum vulgare L.)

MicroRNAs (miRNAs) are short, endogenous and non-protein coding RNAs that are 18-26 nucleotides (nt) in length. The miRNAs have been shown to play important regulatory roles in almost all plant processes, including responses to various stresses. These regulatory functions of the miRNAs are to negatively control the protein coding sequences at posttranscriptional level. The mature miRNAs (18-26 nt) are generated from long (50-550 nt) precursor miRNAs (pre-miRNAs). Mostly the pre-miRNAs have one mature miRNA sequence in the stem region, but few have been reported with more than one mature miRNAs. Such miRNAs are called pre-miRNA cluster. In current research, various computational tools were used for the identification and characterization of new conserved pre-miRNA clusters and their targets in barley (Hordeum vulgare L.). Consequently, a total 18 new pre-miRNA clusters were identified from 17 miRNAs families in barley from total 501,838 express sequence tags (ESTs). These miRNA families were: miR394, 396, 414, 473, 475, 482, 817, 1432, 2118, 2673, 5066, 5070, 5168, 5181, 5201, 5522 and 7757. The miR-5070 was identified as sense and anti-sense cluster and 81 protein targets were identified for pre-miRNA clusters. These protein targets were categorized as: hypothetical protein, metabolism protein, transcription factor, transporter protein, cell signaling protein, growth & development protein and structural proteins. These newly identified pre-miRNA clusters and their 81 targets were reported here for the first time in barley. These results will be a good contribution to fine-tune the regulation of barley for better yields, agronomic traits and stress management.