Computational Identification of Citrus reticulata L. microRNAs and the Cis-Acting Regulatory Elements to Predict the Expression Probability of Their Respective MIR Genes

Abstract

MicroRNA(miRNA), a small non-coding class of RNA that regulates the gene expression, is conserved among several plant species. In the present study, an in-silico approach was adopted to identify miRNA from the known expressed sequences tags (ESTs) of Citrus reticulata L. A total of 17 miRNAs from 23 different ESTs along with their secondary structures and targets were predicted. The identified 63 targets include several transcription factors, proteins that regulate plant growth, development, flowering, and seed development together with stress response. The cis-regulatory element present at the promoter region of the MIR genes of C. reticulata describes their role during light responsiveness, auxin, gibberellins, abscisic acid (ABA), anthocyanin responsiveness, salicylic acid responsiveness, anaerobic induction, circadian control, nitrate dependent regulation of the cell cycle and DNA replication, defense, and stress responsiveness. The present study identifies the miRNAs along with their regulatory elements in C. reticulate. The study will also be useful for the research on identification from the genomic data of different plants and prediction of expression probability of identified MIR genes based on the presence of upstream promoter and other regulatory elements.