Non-coding RNA: a new perspective on the regulation of secondary metabolites in medicinal plants

Medicinal plants are a valuable reservoir of diverse secondary metabolites (SMs), which serve as essential sources for natural drug development. However, the natural production of these bioactive compounds is generally low. Moreover, the biosynthetic processes of these SMs are regulated by a sophisticated network involving transcription factors, post-translational modifications, as well as plant hormones and environmental factors. Recent studies have identified an increasing number of non-coding RNAs (ncRNAs) and confirmed their roles in regulating SM biosynthesis. In this review, we systematically summarize the research progress on the regulation of SM biosynthesis by ncRNAs in medicinal plants, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and phased secondary siRNAs (phasiRNAs). Additionally, we summarize ncRNA‑mediated studies in staple crops, horticultural plants, and woody species to provide references for medicinal plant research. Finally, we discuss future research directions for ncRNAs in medicinal plants, including the construction of spatiotemporal regulatory networks, the application of artificial intelligence (AI)-assisted approaches, the elucidation of molecular regulatory mechanisms, and potential applications of ncRNAs in the standardized production of medicinal plants.