Novel microRNAs associated with the immune response to cucumber mosaic virus in hot pepper (Capsicum annuum L.)

MicroRNAs (miRNAs) are a category of short, highly conserved, noncoding RNAs that modulate various physiological activities correlated with plant growth, stress response, and virus-host interaction. However, the miRNAs associated with cucumber mosaic virus (CMV) resistance in hot pepper (Capsicum annuum L.) remain unexplored. The present work employed small RNA sequencing to compare CMV-infected pepper seedlings with the control seedlings at different time points. The analysis using miRDeep2 software identified 216 known and 34 novel miRNAs from the 12 pepper libraries generated in this study. Further research predicted 3914 targets for these novel miRNAs, of which 3502 were conserved miRNA target genes and 412 were novel miRNA target genes. Functional analysis revealed significant enrichment of these miRNA in ‘plant-pathogen interaction’, ‘ubiquitin-mediated proteolysis’, and ‘metabolic pathways’. Finally, quantitative RT-PCR validated the sRNA sequencing data. These findings set the groundwork for further studies on the CMV resistance mechanisms of pepper.