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.

Biphenyls are unique phytoalexins de novo synthesized in plants in response to pathogen attack. These compounds are found in Maloideae, a subfamily of the Rosaceae. The anti-microbial activities of biphenyls have been reported in a number of studies and they appear to represent an important defense strategy against pathogens common in the Maloideae, such as species in Malus, Pyrus, Sorbus, and Chaenomeles. Here, cell suspension cultures of Sorbus pohuashanensis were established to study biphenyl phytoalexins formation after yeast extract (YE) treatment. An ultra-performance liquid chromatography (UPLC) method coupled with quadrupole time of flight mass spectrometry (Q-TOF-MS) LC−MS/MS was applied to determine the time course of these biphenyl biomarkers accumulation in YE-treated S. pohuashanensis suspension cells. The results of quantitative analyses show the content of Noraucuparin, 2′-Hydroxyaucuparin, and their glycosides initially increased, then decreased over time. The Noraucuparin content reached its highest (225.76 μg·g⁻¹) at 18 h after treatment, 6 hours earlier than that of Noraucuparin 5-O-β-d-glucopyranoside. The content of 2′-Hydroxyaucuparin reached its highest (422.75 μg·g⁻¹) at 30 h after treatment, also earlier than that of its glycoside. The understanding of phytoalexin metabolism in this study may provide a basis for improving Maloideae resistance to pathogens.

Dendrobe (Dendrobium spp.) is a traditional medicinal and edible food, which is rich in nutrients and contains biologically active metabolites. The quality and price of dendrobe are related to its geographical origins, and high quality dendrobe is often imitated by low quality dendrobe in the market. In this work, near-infrared (NIR) spectroscopy sensor combined with porphyrin and chemometrics was used to distinguish 360 dendrobe samples from twelve different geographical origins. Partial least squares discriminant analysis (PLSDA) was used to study the sensing performance of traditional NIR and tera-(4-methoxyphenyl)-porphyrin (TMPP)-NIR on the identification of dendrobe origin. In the PLSDA model, the recognition rate of the training and prediction set of the TMPP-NIR could reach 100%, which was higher than the 91.85% and 91.34% of traditional NIR. And the accuracy, sensitivity, and specificity of the TMPP-NIR sensor are all 1.00. The mechanism of TMPP improving the specificity of NIR spectroscopy should be related to the π-π conjugated system and the methoxy groups of TMPP interact with the chemical components of dendrobe. This study reflected that NIR spectrum with TMPP sensor was an effective approach for identifying the geographic origin of dendrobe.

Root rot caused by Fusarium spp. is the most destructive disease on Atractylodes lancea, one of the large bulks and most common traditional herbal plants in China. In this study, we isolated a bacterial strain, CF3, from the rhizosphere soil of A. lancea and determined its inhibitory effects on F. oxysporum in both in vitro and in vivo conditions. To deeply explore the biocontrol potential of CF3, we sequenced the whole genome and investigated the key pathways for the biosynthesis of many antibiotic compounds. The results revealed that CF3 is a member of Burkholderia ambifaria, harboring two chromosomes and one plasmid as other strains in this species. Five antibiotic compounds were found that could be synthesized due to the existence of the bio-synthesis pathways in the genome. Furthermore, the synthesis of antibiotic compounds should be confirmed by in vitro experiments and novel compounds should be purified and characterized in further studies.

Leonurus japonicus is a vital herb known for its blood-activating and menstruation-regulating properties, with stachydrine being a crucial secondary metabolite contributing to these effects. Enhancing the accumulation of active ingredients is a key concern in cultivation. This study utilized a hydroponic experiment with varying inorganic nitrogen (N) concentrations (supplied as Ca(NO₃)₂·4H₂O and KNO₃) as nutrient substrates, demonstrating that exogenous nitrogen input significantly increased biomass and promoted stachyridine synthesis in L. japonicus over an extended incubation period. Analysis of key intermediates in the stachydrine synthesis pathway suggests that exogenous nitrogen enhanced the amino acid synthesis pathway in primary metabolism, promoting glycolysis and accumulating tricarboxylic acid (TCA) cycle substances, namely, pyruvate and α-ketoglutarate. This, in turn, enhanced the production of stachydrine precursors—glutamic acid and ornithine. Nitrogen’s involvement redirected the amino acid synthesis pathway more towards the alkaloid synthesis pathway. The study confirmed the essential role of nitrogen in promoting the quality formation of L. japonicus and provided initial evidence for the mechanism behind stachydrine formation, offering theoretical and practical insights for improving L. japonicus cultivation technology.