Identification and characterization of long non-coding RNAs regulating flavonoid biosynthesis in Ginkgo biloba leaves

Flavonoids are the main secondary metabolites in Ginkgo biloba leaves. Most previous studies focused on the molecular mechanisms of structural genes and transcription factors regulating flavonoid synthesis. Few reports have examined the long non-coding RNAs (lncRNAs) regulating flavonoid synthesis in G. biloba. Here, we performed high-throughput sequencing of three stages of G. biloba leaves with significant differences in flavonoid contents. We identified 2124 lncRNAs, including 1032 intergenic lncRNAs and 1092 antisense lncRNAs. Enrichment analysis revealed that cis-regulated target genes of upregulated lncRNAs were significantly enriched in the flavonoid biosynthesis pathway. Among these, 28 differentially expressed structural genes in this pathway and 14 key transcription factors may be regulated by multiple lncRNAs. In addition, we found that lncRNAs may act as precursors and endogenous target mimics of miRNAs to indirectly regulate protein-coding genes (PCgenes). More importantly, we found that multiple lncRNAs may serve as the targets of miR156a, miR172a, miR396a, miR828a, and miR858a and participate in the synthesis of ginkgo flavonoids by forming lncRNA (target)–miRNA–PCgene networks. Taken together, our results characterize the differences in the structure and expression levels of G. biloba lncRNAs and protein-coding genes, and demonstrating that lncRNAs may participate in the regulation of biosynthesis of G. biloba flavonoids in several ways.