Profiling and annotation of microRNAs and their putative target genes in chilli (Capsicum annuum L.) using ESTs

• A total of 88 miRNAs (81 miRNA families) were discovered from the mining of 118,572 express sequence tags (ESTs).
• Two miRNA genes were also found as pre-miRNA clusters (can-mir8019 and can-mir8036).
• Nine miRNAs are randomly selected and experimentally validated through RT-PCR.
• Total of 408 protein targets were also predicted for these newly profiled miRNAs.

MicroRNAs (miRNAs) are short, endogenous and non-protein coding RNAs that are 18–26 nucleotides (nt) in length. The main function of the miRNAs is to negatively control the protein coding sequences at post-transcriptional level. By nature, majority of the miRNAs are evolutionarily conserved. This conserved nature provides the logic to predict the new miRNAs orthologus in a number of plant species. In plants, miRNAs are involved in almost all biological processes from growth and development to biotic and abiotic stresses with metabolism and cell signaling. In the current research, various computational tools were used for the profiling and characterization of new conserved miRNAs and their targets in chilli (Capsicum annuum L.). Consequently, a total of 88 miRNAs (belonging to 81 miRNA families) were discovered from the mining of 118,572 express sequence tags (ESTs). In this study, two miRNA genes were also found as pre-miRNA clusters (can-mir8019 and can-mir8036). In addition, nine miRNAs are randomly selected and experimentally validated through RT-PCR. Furthermore, a total of 409 protein targets were also predicted for these newly profiled miRNAs. These predicted protein targets were classified as: transcription factor, stress related, disease related, growth and development, hypothetical protein, transporters, signaling pathways, metabolism and structural protein. All of these newly identified miRNAs were reported in chilli for the first time. These results will serve as reference data to improve the regulation, management, and modification of this economically important plant at the molecular level. This will also help us to improve the chilli plant for production and biotic and abiotic stress tolerance in the near future.

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