Bioinformatics profiling and characterization of potential microRNAs and their targets in the genus Coffea

MicroRNAs (miRNAs) are a class of noncoding small endogenous RNAs with lengths of 18 to 26 nucleotides that have been shown to regulate gene expression at posttranscriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Although thousands of miRNAs have been identified in many species, limited miRNAs have been reported in the genus Coffea, a member of the family Rubiaceae that is endemic to tropical Asia and South Africa. The genus Coffea, whose seeds are known as coffee beans, is used to make coffee. In this study, we identified 51 potential genus Coffea miRNAs, belonging to 51 families, using a well-defined comparative genome-based computational approach in genus Coffea expressed sequences tags. These identified miRNAs potentially target 150 protein-coding genes, which can act as transcription factors and take part in multiple biological and metabolic processes, hypothetical proteins, signal transduction, transporters, growth and development, stress-related processes, structural constituents, and disease-related processes. The results of this research may contribute to the understanding of the miRNA-mediated life processes in the genus Coffea.