Computational identification and characterization of potential miRNAs from Asiatic cotton (Gossypium arboreum L.)

摘要

To date, very few reports of microRNAs (miRNAs) are there in the commercially important diploid Asiatic cotton although there are several reports of miRNAs in upland cotton. MicroRNAs are a large family of 19-26 nucleotides, evolutionary conserved, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in plants as well as animals. Despite the important functions of miRNAs related to the regulation of plant growth and development processes, little is known about the disease responsive miRNA. In the present study, a new pipeline for miRNA analysis using expressed sequence tags (ESTs) based bioinformatics approach has been presented. For this, 64,083 raw EST sequences of Gossypium arboreum were retrieved from EST database in NCBI. Assembled EST contigs database was used to BLAST against Gossypium raimondii miRNA dataset to predict the miRNA and 45 miRNAs of G. arboreum were predicted. Majority of the predicted miRNAs were of 24,23,22and 26 nucleotides in length. The potential targets of these miRNAs were mRNAs encoding enzymes regulating essential plant metabolic pathways including the putative transcription factors, methyltransferases, disease resistance proteins, wound-responsivefamily protein, early nodulin related protein, phosphatase 2C family proteins and mostly are related to the responses to the biotic stresses and stress signaling in plants.