Micro RNA     Send Orders for Reprints to reprints@benthamscience.ae MicroRNA, 2019, 8, 135-146 135 RESEARCH ARTICLE Exploring microRNAs, Target mRNAs and their Functions in Leguminous Plant Arachis hypogaea Anjana Rajendiran 1 , Saravanan Vijayakumar 1,2 and Archana Pan 1,* 1 Centre for Bioinformatics, Pondicherry University, Pondicherry-605014, India; 2 ICMR (Statistics/Bioinformatics), Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India Abstract: Background: MicroRNAs (miRNAs) are a class of small non-coding, endogenous RNAs that regulate gene expression at post-transcriptional level. In plants, miRNAs are usually of 18-24 nucleotide in length and play humongous role by aiding in development, growth, defense, biotic and abiotic stress responses, etc. Objective: Arachis hypogaea is an economically important oil seed crop and human dietary source cultivated mostly in tropical and subtropical regions. In the present study, an initiative was taken to uncover miRNAs, their targets and functions in this important plant species. Method: Comparative genomics strategy coupled with bioinformatics approaches was deployed for the identification of miRNAs, their corresponding targets and functions by exploiting biological da- tabases and tools. Results: The study was able to identify 34 conserved miRNA candidates, belonging to 17 miRNA families, contributed by 23 and 3 precursor miRNAs from A. hypogaea Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS), respectively. As well, 495 EST and 917 unigene se- quences were predicted as targets for the identified miRNAs. Herein, psRNAtarget server and Tar- getFinder tool were used to predict unigene targets, whereas comparative genomics strategy was used for identifying EST targets. Functional annotation of the identified targets revealed that the identified miRNAs regulate mRNAs that participate in key biological and metabolic processes. Pathway en- richment analysis using KEGG database also revealed that they regulate important metabolic path- ways including antibiotic biosynthesis, biosynthesis of unsaturated fatty acids, amino acids metabo- lism and flavonoid biosynthesis. Conclusion: The outcome of the study would aid experimental biologists to focus on these miRNAs to facilitate improved crop development and yield. A R T I C L E H I S T O R Y Received: July 27, 2018 Revised: September 25, 2018 Accepted: October 29, 2018 DOI: 10.2174/2211536608666181105114154 Keywords: Arachis hypogaea, comparative genomics, functional annotation, MicroRNA, precursor miRNA, target. 1. INTRODUCTION MicroRNAs (miRNAs) are small, single-stranded endog- enously expressed non-coding RNAs acting as post transcriptional regulators. They are found to be present in most eukaryotes, including plants. In plants, miRNAs are typically 18-24 nucleotide (nt) in length [1]. These small, single-stranded miRNAs are produced following a series of multistep enzymatic processes, which include transcription, two-step cleavage and unwinding RNA-Induced Silencing Complex (RISC) assembly [2, 3]. Mature miRNAs are known to regulate gene expression of the target messenger RNAs (mRNA) either by triggering degradation or inhibiting *Address correspondence to this author at the Centre for Bioinformatics, Pondicherry University, Pondicherry-605014, India; Tel: +91 413 2654584; E-mail: archana@bicpu.edu.in gene translation through hindering ribosomal movement [4, 5]. It has been reported that plant miRNAs tend to have per- fect or near perfect complementarity with their targets com- pared to animals [6]. This attribute of miRNA-mRNA du- plexes makes it easier to predict miRNA targets in plants compared to animals; many such targets have been identified following this property in different plant species [7]. The understanding of miRNA mediated gene regulations in plant has indicated that miRNAs play an important role in diverse biological processes, including development, stress respons- es, signal transduction, pathogen invasion and metabolism [8]. Thus, during recent years, prediction of miRNAs and their targets has been paid much attention by the scientific community. MiRNAs are initially identified in round worms by forward genetics approach, but till now no plant miRNA is discovered using this method [6]. Since this method is ex- 2211-5374/19 $58.00+.00 © 2019 Bentham Science Publishers