Integrative Analysis of Small RNA and Gene Expression Uncovers a Novel Long-Noncoding MicroRNA Targeting a UDP-Transferase in Camellia chekiangoleosa

Biosynthesis of specific secondary metabolites in plants involves fine regulation of gene expression. Camellia chekiangoleosa has important economic value: the seeds contain high-quality unsaturated fatty acids and the pericarp is rich in tea saponins. As an important posttranscriptional regulator, the role of microRNAs (miRNAs) in controlling secondary metabolism in C. chekiangoleosa is not fully studied. Here, we investigated the role of miRNAs and their targets in the secondary metabolic regulatory network by comprehensively analyzing small RNAs, transcriptomes, and degradomes from different tissues. We identified 168 known miRNAs and 74 novel miRNAs in the C. chekiangoleosa genome and revealed 15 tandem clusters containing 35 miRNAs. By establishing a gene regulatory network containing miRNAs, target genes, and transcription factors, we unravelled the multiplicity of miRNA tissue-specific regulation of gene expression, which may be tightly linked to the synthesis of secondary metabolites. Furthermore, we characterized a novel long-noncoding miRNA gene (cch-miR3633) that targeted a UDP-transferase gene (CchUGT94E5). We showed that, ectopic expression of CchUGT94E5 caused outgrowth of shoot branching and changes in cytokinin contents in Arabidopsis, indicating a potential role of regulating secondary metabolism. This work provides valuable information for the study of miRNA regulation of secondary metabolism.