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.

Fagopyrum dibotrys, being native to southwest China, is widely distributed in Yunnan, Guizhou Provinces and Chongqing City. However, the quality of medicinal materials growing in different origins varies greatly, and cannot meet the market demand for high-quality F. dibotrys. In this study, 648 metabolites were identified, and phenolic compounds of F. dibotrys from different origins were clearly separated by principal component analysis (PCA). Our results suggested that the medicinal differences of F. dibotrys from different origins can be elucidated via the variations in the abundance of the phenolic and flavonoid compounds. We found that the epicatechin, total flavonoids and total tannin content in Yunnan Qujing (YQ) and Yunnan Kunming (YK) were higher than those in Chongqing Shizhu (CS), Chongqing Fuling (CF) and Guizhou Bijie (GB), suggesting that Yunnan Province can be considered as one of the areas that produce high-quality medicinal materials. Additionally, 1,6-di-O-galloyl-β-D-glucose, 2,3-di-O-galloyl-D-glucose and gallic acid could be used as ideal marker compounds for the quality control of F. dibotrys from different origins caused by metabolites, and the F. dibotrys planted in Yunnan Province is well worth exploiting.

Background: The genus Atractylodes, native to East Asia, encompasses several species that serve as sources for the widely used traditional Chinese medicines Atractylodis Macrocephalae Rhizoma and Atractylodis Rhizoma. However, the international trade arouses concern regarding potential confusion and misidentification of Atractylodes species. Objective: A comprehensive understanding of the chemical diversity is crucial for ensuring the quality and exploring the potential variations in medicinal efficacy of Atractylodes. Methods: The GC-MS/MS-based metabolomics and multivariate statistical analysis identified 589 differentially accumulated metabolites across 5 Atractylodes species. Results: A total of 150 metabolites were predicted as potential chemical markers for species differentiation and quality assessment of Atractylodes. According to the metabolic profiles, the species of Atractylodes can be roughly classified into three categories: A. lancea and A. coreana with the volatile oil components being mainly atractylodin and β-eudesmol; A. macrocephala with the biomarker being atractylon; and A. japonica and A. carlinoides lying between the two categories above. Conclusions: Metabolomic results indicated that the metabolic profiles of A. carlinoides and A. macrocephala were similar and distinct from those of the other three species. Sesquiterpenoids were the main chemical components in the rhizome of A. carlinoides, which indicated the potential medicinal value of this plant.

Plant stress memory can provide the benefits of enhanced protection against additional stress exposure. Here, we aimed to explore the responses of recurrent and non-recurrent yeast extract (YE) stresses in Sorbus pohuashanensis suspension cells (SPSCs) at metabolomics and transcriptional levels. Biochemical analyses showed that the cell wall integrity and antioxidation capacity of SPSCs in the pretreated group were evidently improved. Metabolic analysis showed that there were 39 significantly altered metabolites in the pretreated group compared to the non-pretreated group. Based on the transcriptome analysis, 219 differentially expressed genes were obtained, which were highly enriched in plant–pathogen interaction, circadian rhythm–plant, oxidative phosphorylation, and phenylpropanoid biosynthesis. Furthermore, the correlation analysis of the transcriptome and metabolome data revealed that phenylpropanoid biosynthesis involved in the production of biphenyl phytoalexins may play a critical role in the memory response of SPSC to YE, and the key memory genes were also identified, including PAL1, BIS1, and BIS3. Collectively, the above results demonstrated that the memory responses of SPSC to YE were significant in almost all levels, which would be helpful for better understanding the adaptation mechanisms of medicinal plants in response to biotic stress, and laid a biotechnological foundation to accumulate favorable antimicrobial drug candidates from plant suspension cells.

Nitrogen (N) strongly affects plant growth and metabolism. Although ammonium toxicity has been reported, the effects of nitrogen on shikonin biosynthesis remain obscure. In this study, we tested four different concentrations of NH₄⁺ on Arnebia euchroma hairy roots (AEHR) to clarify the influence of NH₄⁺ on the growth of AEHR and on shikonin accumulation in them and the possible mechanisms. The results showed that compared with the 0% NH₄⁺ treatment (only nitrate as a nitrogen source), the 10% NH₄⁺ treatment increased the fresh weight and the dry weight of AEHR and promoted the synthesis of shikonins. In contrast, the 20% NH₄⁺ treatment started to show inhibition effects on the growth of and shikonin accumulation in AEHR, and the 30% NH₄⁺ treatment exhibited the strongest inhibition effects. With an increased percentage of NH₄⁺, the AEHR became shorter and thicker, with more branches. To further elucidate the mechanisms, we analyzed the time course of nitrogen assimilation, the gene expression level of key enzymes involved in shikonin biosynthesis pathway, and the content of various endogenous hormones in the presence of toxic NH₄⁺ concentrations. The results indicated that auxin and cytokinin might regulate the growth and architecture of AEHR under NH₄⁺ toxicity and revealed that the jasmonate level was reduced along with the inhibition of shikonin biosynthesis. This first comprehensive investigation of the effects of the ammonium/nitrate ratio on shikonin biosynthesis not only provides valuable data for optimizing the in vitro culture of A. euchroma and its shikonin production, but also suggests potential fertilizing strategies for its cultivation.

Nitrogen (N) strongly affects plant growth and metabolism. For shikonin biosynthesis, although the ammonium toxicity phenomenon has been reported, the effects of nitrogen on the shikonin synthesis remains obscure. In this study, we carried out four different concentrations of NH4+ treatments on Arnebia euchroma hairy roots (AEHR) to clarify the influence of NH4+ on the growth and shikonin accumulation in A. euchroma and the possible mechanism. The results showed that compared with the 0% NH4+ treatment (only nitrate as nitrogen source), 10% NH4+ treatment increased the fresh weight and the dry weight of AEHR, and promoted the synthesis of shikonins; 20% NH4+ treatment started to show the inhibition effects on growth and shikonin accumulation of AEHR and 30% NH4+ treatment exhibited the strongest inhibition effects. With increased percentage of NH4+, AEHRs became shorter and thicker with more branches. To further elucidate the mechanism, we analyzed the time-course of nitrogen assimilation, gene expression level of key enzymes involved in the shikonin biosynthesis pathway, and contents of various endogenous hormones under NH4+ toxicity condition. Results indicated that auxin and cytokinin might regulate the growth and architecture of AEHR under NH4+ toxicity, and jasmonate level was reduced along with the inhibition of shikonin biosynthesis. This first comprehensive investigation into the effects of ammonium/nitrate ratio on shikonin biosynthesis not only provided valuable data for optimizing the in vitro culture and shikonin production in A. euchroma, but also suggested potential fertilizer strategies for its cultivation.