Mingcheng Wang ^* Shuqiao Zhang Rui Li Qi Zhao ^*

• Chengdu University, Chengdu, China

Medicinal plants are important sources of bioactive specialised metabolites with significant therapeutic potential. Advances in multi-omics have accelerated the understanding of specialised metabolite biosynthesis and regulation. Genomics, transcriptomics, proteomics, and metabolomics have each contributed new insights into biosynthetic gene clusters (BGCs), metabolic pathways, and stress responses. However, single-omics approaches often fail to fully address these complex processes. Integrated multi-omics provides a holistic perspective on key regulatory networks. High-throughput sequencing and emerging technologies like single-cell and spatial omics have deepened our understanding of cell-specific and spatially resolved biosynthetic dynamics. Despite these advancements, challenges remain in managing large datasets, standardizing protocols, accounting for the dynamic nature of specialised metabolism, and effectively applying synthetic biology for sustainable specialised metabolite production. This review highlights recent progress in omics-based research on medicinal plants, discusses available bioinformatics tools, and explores future research trends aimed at leveraging integrated multi-omics to improve the medicinal quality and sustainable utilization of plant resources.