Profiling of miRNAs in Bhut Jolokia (Capsicum chinense) and Kon Jolokia (C. frutescens) of Northeast India

Abstract MicroRNAs (miRNAs) are crucial elements of convoluted gene regulatory network that governs plant development and stress responses. The role of small RNAs (sRNA) especially in C. chinense (Bhut Jolokia) and C. frutescens (Kon Jolokia) of Capsicum genus are still unexplored. Therefore, to identify miRNAs small RNA sequencing was performed from leaf, flower, stem and fruit tissues of C. chinense and C. frutescens. The profiling of small RNAs identified a total of 279 and 254 conserved; along with 490 and 155 novel miRNAs in C. chinense and C. frutescens, respectively. The genomic distribution of miRNAs revealed the extensive genome wide distribution as well as clustering of miRNAs across the twelve Capsicum chromosomes. Synteny analysis provided insights into conservation of high confidence Capsicum miRNAs in Solanaceae family. Furthermore, the expression pattern of 5 differentially expressed and 16 tissue-specific miRNAs was validated through stem-loop qRT-PCR. The target prediction and gene ontology enrichment analysis revealed the possible role of miRNAs in carotenoid biosynthesis, fruit ripening, aroma formation, transcription regulation, signal transduction, and cellular metabolism. About 51 putative Solanaceae–specific miRNAs were predicted which targets diverse range of developmental and disease resistance proteins. The expression analysis demonstrated that several miRNAs were expressed in a tissue-specific/preferential manner indicating their involvement in tissue/organ development. This is the most comprehensive study of miRNA identification in Bhut jolokia and Kon jolokia which would contribute in strengthening the study of miRNA mediated gene regulation involved in growth and development in Capsicum species.