Bioinformatics prediction and annotation of cherry (Prunus avium L.) microRNAs and their targeted proteins

MicroRNAs (miRNAs) are important noncoding regulatory RNAs. They are expressed endogenously and are 18-26 nucleotides in length. These small molecules are conserved evolutionarily within the same kingdom and their conserved nature becomes an important logical tool for the quest of conserved miRNAs in other species by homology search using bioinformatics tools. Cherry (Prunus avium L.) is one of the important and nutritious species of the family Rosaceae, mainly distributed in temperate climate. This research is an attempt to identify and characterize conserved miRNAs in cherry from express sequence tags (ESTs). Bioinformatics analysis of cherry ESTs resulted in the identification of 91 conserved miRNAs belonging to 88 miRNA families. Among the identified miRNAs, two of the conserved miRNAs (pav-miR482 and pav-miR535) were found to be transcribed in the opposite direction of the same genomic locus (sense/antisense orientation). A miRNA (pav-miR482a) was identified as a precursor miRNA (pre-miRNA) cluster while another (pav-mir161) was identified with two overlapping mature miRNA sequences. In addition, highly conserved pre-miRNA was also found, i.e. pav-mir535, which showed 100% query coverage and 98% identity with the peach pre-miRNA ppe-miR535a. Moreover, 14 predicted miRNAs were selected randomly for experimental validation through RT-PCR. Experimental validation of these 14 microRNAs endorses the powerfulness of bioinformatics prediction of miRNAs. The 91 miRNAs were also subjected to study of their 211 protein targets. These were involved in various biological processes including cell signaling, growth and development, transcription factors, and stress management. The results of this research will contribute in understanding the miRNA-mediated life processes in cherry.