Identification of UV-B radiation responsive microRNAs and their target genes in chrysanthemum (Chrysanthemum morifolium Ramat) using high-throughput sequencing

•The contents of several bioactive ingredient increased under UV-B radiation.•UV-B radiation responsive microRNAs were identified.•Key genes for glycolysis were predicated as potential target genes.•Genes involved in the biosynthesis of chlorogenic acids were predicated.•Genes involved in the biosynthesis of flavonoids were predicated. MicroRNAs (miRNA) play a key roles in ultraviolet-B (UV-B) induced accumulation of bioactive ingredients in plants. Chrysanthemum (Chrysanthemum morifolium Ramat) is a popular ornamental herb with numerous biological activities, but its miRNAs and their roles in UV-B-induced active ingredient accumulation remain unexplored. High-throughput miRNA sequencing technology was used to identify miRNAs responsive to UV-B radiation. Four libraries were constructed from Chrysanthemum ‘Xiaoyangju’ leaves harvested at different time points under UV-B radiation. In total, 245 miRNAs belonging to 42 classical families were identified. Under UV-B treatment, 137 miRNAs showed differential expression, including 71 known and 67 novel miRNAs,. In addition, 1,779 unique target genes involving diverse biological processes were predicted for 80 known and 85 novel miRNAs. Three key glycolysis genes, Glyceraldehyde-3-Phosphate Dehydrogenase, Pyruvate Kinase and Glucan Endo-1,3-beta-D-Glucosidase, were predicated as potential target genes of miR396f-5p, PC-5p-294053_21 and miR397a, respectively. Among identified target genes, five key genes involved in the biosynthesis of chlorogenic acids and flavonoids were predicated as potential targets genes of MIR4367-p5, PC-3p-40855_284, MIR393b-p5, and PC-3p-114893_93. The expression of identified miRNAs relating to bioactive ingredient biosynthesis was significantly affected by UV-B radiation, suggesting a strong effect of UV-B radiation on bioactive ingredient accumulation in Chrysanthemum. Interestingly, several miRNAs related to flavonoids biosynthesis such as PC-3p-114893_93 and MIR4367-p5, were inhibited by short-term UV-B radiation, suggesting that the contribution of UV-B to flavonoids accumulation depends on a low dose of UV-B radiation.