The formation of high-quality Chinese medicinal materials is a micro-evolutionary process of multiple genes involving quantitative inheritance under environmental stress. Atractylodes lancea is a traditionally used medicinal plant in China that is broadly distributed and possesses a considerable amount of essential oils. However, to date, limited research has been conducted to characterize the genetics and metabolites of A. lancea shaped by natural variation. Hence, we assembled a high-quality genome of A. lancea, featuring a contig N50 of 1.18 Mb. We further integrated population resequencing of A. lancea and conducted analyses to characterize its genetic diversity, population evolution, and rewiring of volatile metabolites. The natural variation effect exerted significant pressure on A. lancea from different geographic locations, resulting in genetic differentiation among three groups. Correlation analysis of metabolites in A. lancea revealed significant natural variations of terpenoids, heterocyclic compounds, ketones, and esters. We also found that 427 metabolites displayed noteworthy divergence due to directional selection. Additionally, our genome-wide association studies on the metabolome for medicinal quality traits identified several candidate genes, such as AlZFP706 and AlAAHY1, exhibiting significant correlations with atractylodin and hinesol levels, respectively. Overall, this study provides an intricate genomic resource for A. lancea, thereby expanding our understanding of the effect of natural variation on metabolites and facilitating the genetic improvement of its medicinal properties.

Hangju (Chrysanthemum morifolium Ramat.), which has been cultivated for more than 2,000 years in China, is used for traditional Chinese medicine and food, as well as grown as an ornamental plant. I...

Background: Cultivation environments impose distinct abiotic and biotic stresses that act as primary drivers reshaping the metabolic profile and microbiome assembly of medicinal plants. This study investigates the impact of simulative habitat versus arched greenhouse cultivation on the synthesis of bioactive ginsenosides and the associated root microbiome structure in Panax ginseng. Methods: A combined metabolomics and microbiomics approach was applied to compare ginsenoside accumulation and rhizosphere microbial community composition under the two cultivation modes. Results: Ginseng from simulative habitat cultivation exhibited significantly higher ginsenoside content, particularly ginsenoside Re, compared to arched greenhouse cultivation, with this advantage being more pronounced in long-term cultivation. Microbiome profiling revealed that specific taxa, including Bradyrhizobium, were strongly enriched in simulative habitats and positively correlated with enhanced ginsenoside accumulation, suggesting a microbiome-mediated mechanism for metabolic plasticity. In contrast, arched greenhouse cultivation was associated with a more complex microbial structure characterized by increased negative interactions, which may compromise metabolic quality. Conclusions: These findings, utilizing multi-omics correlations, provide a theoretical basis for optimizing Panax ginseng quality through ecological cultivation strategies that leverage stress-responsive microbe–metabolite interactions.

Background/Objective: Anoectochilus roxburghii, a high-value medicinal orchid, faces significant challenges in quality standardization during large-scale tissue culture due to a lack of understanding of the underlying molecular mechanisms. This study aimed to compare “Jianlan No.2” plantlets cultured under a conventional tissue culture system (CK) and a sugar-free tissue culture system (TD), to elucidate the phenotypic and molecular basis for quality improvement. Methods: A systematic comparison was conducted. Phenotypic traits of plantlets from both systems were measured. Integrated transcriptomic (RNA sequencing) and untargeted metabolomic analyses were employed to identify the molecular differences at the gene expression and metabolite accumulation levels. Results: TD-grown seedlings exhibited significantly superior growth characteristics, including greater plant height, higher rooting rate, and improved transplant survival. Transcriptomic analysis identified 416 differentially expressed genes (DEGs) (44 upregulated, 372 downregulated in TD), which were significantly enriched in pathways related to cell wall organization, apoplast, and photosynthesis. Sixteen key genes were pinpointed as closely associated with seedling growth and metabolic regulation. Metabolomic profiling revealed 502 differentially accumulated metabolites (DAMs), with significant perturbations primarily in phenylpropanoid biosynthesis and terpenoid metabolism. Conclusions: The sugar-free tissue culture system enhances A. roxburghii seedling quality by coordinately modulating photosynthetic capacity, carbon metabolism, and the biosynthesis of key secondary metabolites. These findings provide a crucial molecular foundation for optimizing tissue culture protocols and advancing the standardized, high-quality cultivation of this valuable medicinal plant.