In silico Characterization of microRNAs and Their Target Transcripts from Cranberry (Vaccinium macrocarpon)

Abstract

MicroRNAs (miRNAs) are highly conserved, non-coding, 20–24 nucleotides long RNA molecules that play important regulatory roles in plants and animals. Due to several limitations involved in the experimental validation of potent miRNAs, in silico prediction of miRNAs and their target(s) from various organisms have been successfully employed. Cranberries are one of the healthiest fruits due to their high nutrient and antioxidant contents. In this study applying genome-wide computational-based approaches and following a set of strict filtering criteria a total of 23 potentially conserved microRNAs belonging to 15 families were identified from cranberry. All the precursors of identified miRNAs formed stable minimum free energy (MFE) stem-loop structure as their orthologues form and possessed high minimum free energy index (MFEI) values. psRNATarget tool detected a total of 92 potential miRNA targets including binding proteins, transcription factors, kinases that are involved in biosyntheses, different metabolic processes, and signal transduction. Among the detected targets, 9 targets (SPLs, proline-rich family proteins, F-Box proteins, HD proteins, Scarecrow proteins, zinc finger proteins, cytochrome P450, sulfate transporters and ABC transporters) were found to have a specific role in phytochemical biosynthesis. To the best of our knowledge, this is the first report of cranberry microRNAs and their targets.