Identification and expression analysis of microRNA in peanut (Arachis hypogaea)



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MicroRNAs (miRNAs) are a class of 21-24 nucleotide (nt) long endogenous non-coding RNAs that negatively regulate the expression of protein-coding genes at post-transcriptional or translational stages. To date, more than 5500 miRNAs have been identified in about 70 different plant species with new reports appearing weekly, as next-generation sequencing projects are published. In plants, other than their developmental regulatory functions, little is known about miRNA roles in abiotic stresses. The reports of new miRNAs expressed under specific environmental conditions suggest that the number of miRNAs discovered to date are far fewer than their actual numbers. There are only 21 miRNA families from peanut that are currently registered with miRBase. In the present study, I aimed at discovering new miRNAs in peanut and characterizing their expression in response to abiotic stresses. A small RNA library from heat stressed peanut leaf tissue was sequenced using the Sequencing by Oligonucleotide Ligation and Detection or SOLiD® platform. A total of 55 new miRNA sequences were identified with 38 belonging to known miRNA families and 5 matching putatively peanut-specific miRNAs reported previously. The remaining 13 sequences represent putative new miRNAs families in peanut. I was able to detect four novel candidate miRNAs (pnut-miRc3, pnut-miRc5, pnut-miRc8 and pnut-miR c12) on a small RNA blot and showed that 3 miRNAs (pnut-miRc3, pnut-miRc5, pnut-miRc8) are peanut specific by in silico and wet lab approaches. Several peanut-specific miRNAs responded differentially to abiotic stresses. miRNA targets were predicted using TargetFinder and psRNAtarget. A subset of the targets were validated using using RLM-RACE.



miRNA, Arachis hypogaea, Abiotic stress