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.)

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Abstract 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.