Multi-omics Insights into the Effects of Region and Growth Period on the Bioactive Compounds of Angelica sinensis (Oliv.) Diels

Angelica sinensis, a traditional medicinal herb, exhibits efficacy quality variations strongly tied to geographical origin and the rhizosphere microbiome composition, yet the microbial drivers of its medicinally bioactive compounds synthesis in authentic versus adjacent regions remain poorly understood. Here, we integrated transcriptomic profiling of plant tissues with 16S rRNA (bacteria) and ITS (fungi) sequencing of rhizosphere soils across multiple growth stages in authentic and near-authentic producing regions. By coupling those dates with targeted metabolomics and soil property analysis. Our results revealed significant regional and growth-stage variations in bioactive compounds and soil properties. Specifically, we identified 2,367 DEGs, 417 bacterial ASVs, and 295 fungal ASVs with differential abundance. Key genera, including Vicinamibacter and Bacillus (bacteria) and Bisifusarium and Longitudinalis (fungi), were found to potentially play important roles in secondary metabolite production. Functional disparities (e.g., chitinolysis, fermentation pathways) were observed, and co-occurrence networks demonstrated tight linkages between plant genes and microbiota. Critically, soil parameters such as organic matter, total nitrogen, and soil alkaline phosphatase were identified as key factors influencing the microbial community structure. Furthermore, the rhizosphere microbiome appears to modulate nutrient absorption, thereby affecting bioactive compound accumulation. Collectively, our multi-omics analysis elucidates the mechanistic influence of region and growth stage on A. sinensis quality, offering new insights for optimizing its cultivation and efficacy across diverse regions.