MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs produce by cell endogenously. They are 18–26 nucleotides in length and play important roles at the post-transcriptional stage of gene regulation. Evolutionarily, miRNAs are conserved and their conservation plays an important role in the prediction of new miRNAs in different plants. Wheat (Triticum aestivum L.) is an important diet and consumed as second major crop in the world. This significant cereal crop was focused here through comparative genomics-based approach to identify new conserved miRNAs and their targeted genes. This resulted into a total of 212 new conserved precursor miRNAs (pre-miRNAs) belonging to 185 miRNA families. These newly profiled wheat’s miRNAs are also annotated for stem-loop secondary structures, length distribution, organ of expression, sense/antisense orientation and characterization from their expressed sequence tags (ESTs). Moreover, fifteen miRNAs along with housekeeping gene were randomly selected and subjected to RT-PCR expressional validation. A total of 32927 targets are also predicted and annotated for these newly profiled wheat miRNAs. These targets are found to involve in 50 gene ontology (GO) enrichment terms and significant processes. Some of the significant targets are RNA-dependent DNA replication (GO:0006278), RNA binding (GO:0003723), nucleic acid binding (GO:0003676), DNA-directed RNA polymerase activity (GO:0003899), magnesium ion transmembrane transporter activity (GO:0015095), antiporter activity (GO:0015297), solute:hydrogen antiporter activity (GO:0015299), protein kinase activity (GO:0004672), ATP binding (GO:0005524), regulation of Rab GTPase activity (GO:0032313) Rab GTPase activator activity (GO:0005097), regulation of signal transduction (GO:0009966) and phosphoprotein phosphatase inhibitor activity (GO:0004864). These findings will be helpful to manage this economically important grain plant for desirable traits through miRNAs regulation.

MicroRNAs (miRNAs) are short non-protein coding RNAs made up of 18 to 26 nucleotides and produced in a cell endogenously. Most of them are conserved in nature evolutionally and thus providing a logical basis for the prediction of novel miRNAs and their clusters in many plants. In this research, structural and functional approaches have been combined to make prediction of novel miRNA clusters and their targets in wheat. The total numbers of detected novel miRNA clusters were 21 related to 19 miRNA families in wheat.

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).