In silico identification and characterization of microRNAs based on EST and GSS in orphan legume crop, Lens culinaris medik. (Lentil)

Abstract

MicroRNAs (miRNAs) are a class of endogenous non-coding, small RNAs that are associated with the regulation of gene expression in eukaryotes. In plants, few miRNAs are highly conserved, that may have the same ancestor in the early stages of evolution. This fact allows the detection of conserved miRNAs in various plant species, especially in those that lack genome sequence information. Though the draft genome of the orphan crop, Lens culinaris Medik. (Lentil) is published, its complete genome assembly is still underway. In this computational study, an EST and GSS based comparative genomics approach were conducted to identify miRNAs in Lentils. The adopted approach was on the basis of a search for sequence similarity followed by series of filtering steps to provide reliable and precise results, eliminating the false-positive predictions. This study reports 24 miRNAs from 10,190 ESTs and 715 GSSs in Lentil. Further, it was also sought to pinpoint the 83 likely target genes of Lentil miRNAs and their most probable functions using Legume Information Resource (LIS) annotation pipeline. The newly identified miRNAs were mainly found to regulate the genes that encode transcription factors and key enzymes involved in metabolic processes as well as oxidation-reduction processes. Many of target genes were found to have an association with plant growth and development, stress response, defense and hormone signaling pathways. The miRNAs accounted is presumed to advance Lentil miRNAome in future as this computational study puts forward, first-ever, view towards miRNA research in Lentil.