Exploring Family Rosaceae in Terms of MicroRNAs and their Targeted Proteins

Abstract

MicroRNAs (miRNAs) are an important class of noncoding regulatory RNAs. They are endogenous in nature and their length ranges from 18-26 nucleotides. They perform important functions in plants and animals during growth, organogenesis, transgene inactivation, cell signaling processes, disease development and defense against the attacking viruses and bacteria. These small molecules are evolutionarily conserved from species to species within the same kingdom and their conserved nature becomes an important logical tool for the hunt of new conserved miRNAs in other species by homology search. Rosaceae is an important angiospermic family of great economic importance. It comprises of over 100 genera and 3,000 species and contains a variety of agricultural species that are both biologically and economically important. Few miRNA have been reported in peach and apple but apricot, cherry and Rosa spp remain neglected in this regard. This research is an attempt to identify and characterize new conserved miRNAs in some important plants of Rosaceae, i.e. apple, apricot, cherry and three species of rose. This study resulted in identification and characterization of 203 new conserved miRNAs belonging to 193 miRNA families from six plants of Rosaceae. A total of 339 targets were also predicted for the identified miRNAs which are proteins of versatile nature. The identified miRNAs contain two cluster miRNAs (mdm- miR3630 and pav- miR482a) and one overlapping cluster miRNA (pav-miR161). Six miRNAs (mdm-miR172, mdm-miR403, mdm-miR3635, mdm-miR6271, pav-miR535, pav- miR482) were predicted on both the sense and antisense strands. Two miRNAs from cherry (pav-miR2084 and pav-miR2085) were found on sense and antisense strands of the same EST. Three miRNA precursors, one each from apple, apricot and cherry (i.e. mdm- mir6271, par-mir6271 and pav-mir535) were found to be highly similar with their reference orthologues. To our knowledge this is the first report of miRNA precursors to be highly conserved in rosaceaous plants and this would open new vistas for miRNA research community. The results of this research would contribute to improve the nutritional and agronomic aspects in apple, apricot, cherry and rose. These findings will also be valuable in understanding various miRNA mediated life processes i.e. metabolism, genetic temporal mechanism, signal transduction and Pathogen Associated Molecular Patterns (PAMPs) in plants.