Integrated mRNA and miRNA omics reveal the regulatory role of UV-B radiation in active ingredient biosynthesis of Chrysanthemum morifolium Ramat

Ultraviolet-B (UV-B) is an effective elicitor that enhances bioactive ingredient biosynthesis in different plants. Chrysanthemum morifolium Ramat (C. morifolium) is a well-known herbal medicine and beverage material, which is cultivated in many Asian countries and regions. The C. morifolium inflorescences are the main accumulation sites for active ingredients, which include flavonoids and chlorogenic acid. However, the molecular mechanisms underlying UV-B-mediated bioactive ingredient biosynthesis in C. morifolium inflorescences remain largely unknown. High-throughput sequencing technologies have been applied to identify the messenger RNAs (mRNAs) and microRNAs (miRNAs) responsive to UV-B radiation in C. morifolium inflorescences. Many UV-B responsive genes are enriched in flavonoid, unsaturated fatty acid, phenylpropanoid, and carotenoid biosynthesis pathways. In this study, we identified 169 miRNAs belonging to 38 typical families were detected in our constructed libraries. In total, 1954 unigenes were predicted to be targets of 118 miRNAs. Six miRNAs, PC-5p-7136_1319, PC-3p-78379_156, ath-MIR414-p5_2ss2CT21AC, PC-3p-154888_69, nta-miR171a_2ss8GT18GA and htu-miR403a were involved in the regulation of active ingredient biosynthesis by targeting 4CL-like 5/9, CYP81E8, UGT91D1 and UGT72B1 genes. Five miRNAs, PC-5p-79_56613, ath-miR858a_L-1, ath-MIR414-p5_2ss15AC18AT, ath-MIR414-p5_2ss2CT21AC, and aly-miR393a-5p were involved in regulation of flavonoid biosynthesis by targeting MYB-bHLH complex-related transcription factor genes. Our data provides a platform for identifying mRNAs and miRNAs involved in the UV-B-induced accumulation of bioactive ingredients in C. morifolium inflorescences.