Computational identification and functional annotation of microRNAs and their targets from expressed sequence tags (ESTs) and genome survey sequences (GSSs) of coffee (Coffea arabica L.)

• 20 potential regulatory miRNAs were predicted from Coffea arabica ESTs and GSSs with an average MFEI of 0.85.
• miR482/miR2118 super family that plays role in defence response was identified.
• Functional redundancy among miRNAs and multi-miRNA based control was observed.
• Phylogenetic tree generated for the miRNAs belonging to family miR393, miR390, and miR397.
• The most over represented GO term in biological process was response to abiotic stress with 22 target genes associated with it.

MicroRNAs (miRNAs) are conserved, small non-coding endogenous RNAs, which are typically 21–24 nucleotides in length and play a pivotal role in post transcriptional gene regulation either by translational repression or cleavage. The regulation of target genes by miRNA has a central role in plant growth and development as well as in stress condition; however, only a few reports on coffee miRNA functions have been published. In the present study, we report the computational identification of miRNAs and their targets from expressed sequence tags (ESTs) and genome survey sequences (GSSs) of Coffea arabica as well as functionally annotated the target genes based on Gene ontology terms (GO). By following stringent filtering criteria, a total of 20 new potential miRNAs belonging to 13 different miRNA families (miR393, miR390, miR397, miR482, miR2118, miR414, miR1879, miR1134, miR1110, miR533, miR5809, miR426 and miR5212) were identified through homology search. The psRNATarget server predicted 142 potential target genes for 17 miRNAs and their probable functions were illustrated. Most of the predicted target genes encoded transcription factors and genes involved in plant growth and development, signal transduction, metabolism, defense and stress responses. The result from this study will shed light on understanding the functions of miRNAs in C. arabica.