mRNA-lncRNA-miRNA Co-Regulates the Accumulation of Flavonoids in Ginkgo biloba in Response to UV-B Stress

Flavonoids are key secondary metabolites involved in plant stress responses. As ultraviolet (UV) radiation intensity increases, plants experience heightened UV stress. To elucidate Ginkgo biloba's molecular adaptation to ultraviolet-B (UV-B) stress, we subjected G. biloba seedlings to daily UV-B irradiation at 10 kJ/m². The total flavonoid glycoside content in leaves increased significantly by Day 13 (2.64-fold compared to the CK), with quercetin accounting for over 90% of the accumulated flavonoids. Transcriptome analysis identified 3652 differentially expressed genes (DEGs), 209 lncRNAs (DElncRNAs), and 52 miRNAs (DEmiRNAs). Notably, UV-B radiation upregulated key genes involved in flavonoid biosynthesis, including the F3'H family gene evm.model.chr2.812 and the MYB transcription factor (TF) evm.model.chr11.568. Trans-regulation analysis suggested lncRNAs modulate target genes: MSTRG.5750.1 and MSTRG.13336.1 potentially enhance evm.model.chr2.812 and evm.model.chr11.568 expression, while UV-B-repressed MSTRG.845.1 and MSTRG.3390.1 indirectly upregulated them. A ceRNA network revealed nine regulatory pairs, though associated miRNAs (gbi-miR-nov634-3, gbi-miR-nov789-3p) exhibited low abundance, indicating minor roles in UV-B response. These findings provide insights into the transcriptional regulation of flavonoid biosynthesis in G. biloba under UV-B stress, advancing understanding of plant secondary metabolic adaptation.