Identification of Conserved miRNAs and Their Target Genes in Faba Bean by EST Based Homology Analysis

Abstract

MicroRNAs (miRNAs) are a class of endogenous, non-coding short RNAs, around 21 nucleotides (nt) in length found in eukaryotic cells and some viruses. To date, miRNAs are identified in several plant species through experimental and computational approaches where they play important roles in growth and development, metabolism, stress responses by guiding mRNA cleavage or repressing translation. Although the faba bean (Vicia faba) is an important source of protein widely used for human and animal nutrition, not a single miRNA has been identified in it up till now. Evolutionary conserved characteristics of plant miRNAs allow the identification of conserved plant miRNAs by homology analysis. The aim of this study is the identification and characterization of miRNAs in faba bean using the EST based homology analysis approach. For computational identification of novel miRNAs in faba bean, 8496 known and unique plant miRNAs from 73 plant species were searched for homology against 20697 expressed sequence tags (EST) and 577 genome survey sequences (GSS). Candidate miRNAs including protein coding sequences were recognized following the miRNA criteria of secondary structure and biogenesis. In this study, 262 candidate miRNAs belonging to 143 miRNA families have been identified for the first time in faba bean. Moreover, psRNATarget server predicted 712 potential target genes of these candidate miRNAs from faba bean. Predicted target genes seem to be involved in the regulation of several important biological processes. The results of this study will contribute to further research on miRNAs, leading to an improved understanding of the role miRNAs play in biological processes and the underlying environmental stress related molecular mechanisms of faba bean.

Keywords

• Computational identification,Expressed sequence tag (EST),miRNA,Target genes,Faba bean,Vicia faba

Kaynakça

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