Non-coding RNAs (ncRNAs) that were once considered “dark matter” or “transcriptional noise” in genomes are research hotspots in the field of epigenetics. The most well-known microRNAs (miRNAs) are a class of short non-coding, small molecular weight RNAs with lengths of 20–24 nucleotides that are highly conserved throughout evolution. Through complementary pairing with the bases of target sites, target gene transcripts are cleaved and degraded, or translation is inhibited, thus regulating the growth and development of organisms. Unlike miRNAs, which have been studied thoroughly, long non-coding RNAs (lncRNAs) are a group of poorly conserved RNA molecules with a sequence length of more than 200 nucleotides and no protein encoding capability; they interact with large molecules, such as DNA, RNA, and proteins, and regulate protein modification, chromatin remodeling, protein functional activity, and RNA metabolism in vivo through cis- or trans-activation at the transcriptional, post-transcriptional, and epigenetic levels. Research on plant lncRNAs is just beginning and has gradually emerged in the field of plant molecular biology. Currently, some studies have revealed that lncRNAs are extensively involved in plant growth and development and stress response processes by mediating the transmission and expression of genetic information. This paper systematically introduces lncRNA and its regulatory mechanisms, reviews the current status and progress of lncRNA research in plants, summarizes the main techniques and strategies of lncRNA research in recent years, and discusses existing problems and prospects, in order to provide ideas for further exploration and verification of the specific evolution of plant lncRNAs and their biological functions.

Ginkgo biloba (ginkgo) leaves have medicinal value due to their high levels of secondary metabolites, such as flavonoids. We found that the flavonoid content in ginkgo leaves increases significantly at high altitudes (Qinghai-Tibet Plateau). Considering that high UV-B radiation is among the key environmental characteristics of the Qinghai-Tibet Plateau, we carried out simulated UV-B treatments on ginkgo seedlings and found that the flavonoid content of the leaves increased significantly following the treatments. Combined with results from our previous studies, we determined that the transcription factor GbHY5 may play a key role in responses to UV-B radiation. Overexpression of GbHY5 significantly promoted the accumulation of flavonoids in both ginkgo callus and Arabidopsis thaliana. Furthermore, yeast two-hybrid and real-time quantitative PCR showed that GbHY5 promoted the expression of GbMYB1 by interacting with GbMYB1 protein. Overexpression of GbMYB1 in ginkgo callus and A. thaliana also significantly promoted flavonoid biosynthesis. GbFLS encodes a key enzyme in flavonoid biosynthesis, and its promoter has binding elements of GbHY5 and GbMYB1. A dual-luciferase reporter assay indicated that while GbHY5 and GbMYB1 activated the expression of GbFLS individually, their co-expression achieved greater activation. Our analyses reveal the molecular mechanisms by which the UV-B-induced GbHY5-GbMYB1-GbFLS module promotes flavonoid biosynthesis in ginkgo, and they provide insight into the use of UV-B radiation to enhance the flavonoid content of ginkgo leaves.

Dendrobium huoshanense is both a traditional herbal medicine and a plant of high ornamental and medicinal value. We used transcriptomics and metabolomics to investigate the effects of growth year on the secondary metabolites of D. huoshanense stems obtained from four different years of cultivation. In this study, a total of 428 differentially accumulated metabolites (DAMs) and 1802 differentially expressed genes (DEGs) were identified. The KEGG enrichment analysis of DEGs and DAMs revealed significant differences in “Flavonoid biosynthesis”, “Phenylpropanoid biosynthesis” and “Flavone and flavonol biosynthesis”. We summarize the biosynthesis pathway of flavonoids in D. huoshanense, providing new insights into the biosynthesis and regulation mechanisms of flavonoids in D. huoshanense. Additionally, we identified two candidate genes, FLS (LOC110107557) and F3’H (LOC110095936), which are highly involved in flavonoid biosynthesis pathway, by WGCNA analysis. The aim of this study is to investigate the effects of growth year on secondarily metabolites in the plant and provide a theoretical basis for determining a reasonable harvesting period for D. huoshanense.

Dendrobium moniliforme (L.) Sw. is a valuable herbal crop, and flavonoids are primarily distributed as active ingredients in the stem, but the composition and synthesis mechanisms of flavonoids in different growth years are not clear. The accumulation of flavonoids in D. moniliforme from four different years was investigated, using a combined metabolomics and transcriptomics approach in this study. The phenylpropanoid and flavonoid biosynthetic pathways were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). The widely targeted metabolomics technique revealed a total of 173 kinds of flavonoid metabolites. The metabolomics data confirmed the trend of total flavonoids (TF) content in stems of D. moniliforme, with chalcone, naringenin, eriodictyol, dihydroquercetin, and other flavonoids considerably up-accumulating in the third year. Twenty DEGs were detected that regulate flavonoid synthesis and the expression of these genes in different growth years was verified using real-time quantitative PCR (qRT-PCR). Furthermore, a comprehensive regulatory network was built for flavonoid biosynthesis and it was discovered that there is one FLS gene, one CCR gene and two MYB transcription factors (TFs) with a high connection with flavonoid biosynthesis by weighted gene co-expression network analysis (WGCNA). In this study, the correlation between genes involved in flavonoid biosynthesis and metabolites was revealed, and a new regulatory mechanism related to flavonoid biosynthesis in D. moniliforme was proposed. These results provide an important reference for the farmers involved in the cultivation of D. moniliforme.

Flavonols are important secondary metabolites that enable plants to resist environmental stresses. Although MYB regulation of flavonol biosynthesis has been well studied, the lncRNA-MYB networks involved in regulating flavonol biosynthesis remain unknown. Ginkgo biloba is rich in flavonols, which are the most important medicinal components. Based on multi-omics data and phylogenetic trees, we identified GbMYB11 as a potential key transcription factor regulating flavonol biosynthesis. Overexpression and VIGS experiments confirmed that GbMYB11 acts as a pivotal positive regulator in flavonol biosynthesis. In the transcriptome of calli overexpressing GbMYB11, we identified significant upregulation of GbF3’H and GbFLS in the flavonol biosynthetic pathway. Yeast one-hybrid and dual-luciferase assays demonstrated that GbMYB11 enhances the expression of GbF3’H and GbFLS by binding to their promoters. Interestingly, we identified LncNAT11, an antisense lncRNA complement to GbMYB11, which negatively regulates flavonol biosynthesis by repressing the expression of GbMYB11. Consequently, we established the LncNAT11-GbMYB11-GbF3’H/GbFLS module as a critical regulator of flavonol biosynthesis in G. biloba, and further elucidated that this module can mitigate the accumulation of reactive oxygen species by modulating flavonol biosynthesis during salt stress. These findings unveil a novel mechanism underlying flavonol biosynthesis and a lncRNA-MYB mediated salt stress tolerance strategy in plants.