Herbal powder, a common dosage form in traditional Chinese medicine, requires rigorous authenticity assessment to ensure medicinal quality and therapeutic efficacy. In this study, we proposed an artificial intelligence (AI) assisted digital fingerprint strategy for rapid detection of herbal powder adulteration, using Bajiaohuixiang (BJHX) as a case. The intelligent algorithms combined with digital image recognition (DIR) and near-infrared spectroscopy (NIRS) techniques achieved effective discrimination in both binary and seven-class classification of adulteration. The optimized bidirectional long short-term memory network delivered good performance, which achieved accuracies of 96.11% and 80.00% using the DIR dataset, and 94.44% and 88.10% using the NIRS dataset, for binary and seven-class classification, respectively. Multimodal data fusion significantly enhanced performance, yielding classification accuracies of 97.22% and 91.90% for the two tasks, respectively, and a quantitative model with coefficient of determination of 0.8807, root mean square error of 0.0560, and mean absolute error of 0.0443. The strategy's robustness was confirmed through external validation, where only one out of multiple commercial and laboratory-prepared samples was flagged as potentially adulterated. Furthermore, greenness assessment using Analytical Greenness Calculator (AGREE, 0.92), Analytical Greenness Metric of Sample Preparation (AGREEprep, 0.90), and Blue Applicability Grade Index (BAGI, 80) frameworks confirmed its environmental sustainability and practical applicability. Overall, this work highlights the significant potential of integrating AI with DIR and NIRS as a rapid, accurate, and green tool for herbal powder authentication.

Codonopsis root is widely recognised as a plant with medicinal applications across various Asian countries. According to traditional treatment, Codonopsis roots may undergo a post-ripening phase to improve their therapeutic efficacy and commercial value. However, the underlying metabolic mechanisms driving quality formation during this process remain poorly understood. In this study, untargeted metabolomics was employed to investigate dynamic metabolite changes throughout the post-ripening. The findings indicate how post-ripening contributes to the quality of Codonopsis roots and reveal its close association with osmotic stress induced by dehydration. Over 2000 metabolites were identified, with fatty acid, amino acid, and carbohydrate metabolism actively involved in quality formation. Furthermore, both elevated temperature and kneading treatments were found to modulate metabolic changes during post-ripening by intensifying osmotic stress, thereby exerting a positive effect on the quality formation of Codonopsis roots. In addition, based on metabolomics data and insights from phenylpropanoid glycoside metabolism and the crepenynate pathway, dynamic regulatory mechanisms underlying the biosynthesis of key bioactive metabolites, including polyacetylenes and tangshenoside I, were systematically analysed. This study provides mechanistic insights into the metabolic basis of quality formation in Codonopsis root and offers a theoretical foundation for optimising post-harvest treatment to improve product quality and commercial value.

Salt stress affects the growth, quality, and secondary metabolism of medicinal plants, but its effects on essential oil biosynthesis in Schizonepeta tenuifolia remain unclear. In this study, a salt stress model was established for Schizonepeta tenuifolia (Benth.) Briq. to investigate changes in growth, monoterpenoid accumulation, non-targeted metabolism, and transcriptional profiles. To further clarify the regulatory mechanism of monoterpenoids biosynthesis, the MYB family members were identified at the genome-wide level, and candidate regulators were screened based on the expression patterns and promoter features of StL3OH (limonene -3-hydroxylase). Among them, StMYB71 and StMYB8774 were identified as candidate regulators of monoterpene biosynthesis. Functional analysis indicated that both transcription factors negatively regulated StL3OH expression by binding to the MYBHv1 cis-element in its promoter. These findings improve our understanding of the salt stress response and transcriptional regulation of monoterpene biosynthesis in S. tenuifolia and provide a basis for the future improvement of Schizonepetae Herba quality and salt tolerance.

As the cost of genome sequencing continues to decline, an increasing number of plant genomes are being sequenced and assembled. This progress allows for the comparison of synteny and microsynteny among genomes and gene clusters across various species, facilitating the exploration of their evolutionary relationships.In this chapter, we describe current methods for analyzing collinearity and synteny among multiple genomes using existing tools from JCVI. We also present a detailed case study that illustrates these methods, utilizing data from four plant genome datasets.

Sparganium stoloniferum tubers (SL), known medicinally as Sparganii Rhizoma, are commonly considered superior at the winter-harvest stage, when they show the traditional quality traits of heavy weight and firm texture. However, the developmental basis of this quality phenotype remains insufficiently understood. This study aimed to determine how tissue organization, cell-wall architecture, starch deposition, and related transcriptional patterns are associated with winter-harvest quality in SL. By comparing SL at different developmental stages, we found that maturation was accompanied by reduced moisture content, increased tuber density, higher parenchyma cell density, progressive cell-wall thickening, and marked starch accumulation. Laser scanning confocal microscopy (LSCM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM) observations further revealed thickened multilamellar cell walls and abundant clustered or compound-like starch bodies in mature SL. Starch isolated from mature SL displayed an A-type crystalline pattern, short-range order, and high gelatinization and pasting temperatures, indicating an ordered and thermally stable starch matrix. Cell-wall Fourier-transform infrared spectroscopy (FTIR) and solid-state nuclear magnetic resonance (NMR) analyses showed a predominantly polysaccharide-rich framework with subtle maturation-associated changes in aromatic- and methoxy-associated wall signals. Transcript-guided pathway analysis, supported by reverse transcription quantitative polymerase chain reaction (RT-qPCR)validation, suggested developmental shifts in carbohydrate metabolism, lipid-related metabolism, and gibberellin-associated transcriptional patterns. Together, these findings indicate that winter-harvest quality in SL is associated with coordinated tissue consolidation, cell-wall maturation, starch deposition, and transcriptional reprogramming, providing a structural and molecular framework for understanding the traditional firm-texture trait of S. stoloniferum.

Fritillariae Thunbergii Bulbus (FTB) is a widely-used herb with significant nutritional and medicinal value. However, the increasing prevalence of adulterated FTB powder (FTBP) in commercial markets has compromised product quality and hindered sustainable industry development. This study developed an integrated strategy combining digital image (DI) analysis and Fourier transform near-infrared (FT-NIR) spectroscopy with intelligent algorithms to detect and quantify FTBP adulterants. The image and spectral data of FTB were used to establish classification models using single and fused datasets by traditional pattern recognition methods, machine learning, and deep learning algorithms. The commercial FTBs were used to validate the developed models. Quantitative regression models were developed using partial least squares (PLS) to predict the concentrations of adulterants in FTB. Traditional chemometrics revealed that DI and NIR dataset could initially distinguish FTBP and its adulterants. Particle swarm optimization-convolutional neural network (PSO-CNN) algorithms demonstrated superior performance by feature-level data fusion (F-LDF), achieving accuracy of 100%. External validation confirmed perfect discrimination of commercial FTBP using DI and NIR data, with predictive rates of 100%. For quantitative analysis, PLS regression yielded exceptional prediction performance, with the ratio of prediction to deviation values reaching 19.69, 7.37, and 6.09 for corn starch, soybean flour, and wheat flour adulteration using F-LDF data. This study established a rapid, nondestructive, and reliable strategy for FTB authentication, with potential applications in quality control of other herbs and spices.

Phenolic acids and flavonoids are major bioactive constituents of Sparganium stoloniferum tubers (SL), yet their spatial organization within this medicinal organ remains insufficiently characterized, limiting understanding of how anatomical structure relates to metabolite distribution. To address this, we integrated mass spectrometry imaging (MSI), non-targeted LC–MS and targeted LC–MS/MS metabolomics, and reverse transcription quantitative polymerase chain reaction (RT–qPCR) analysis to characterize the spatial patterns of phenylpropanoid- and auxin-related metabolites and selected transcripts in SL. MSI and non-targeted LC–MS profiling showed that phenylpropanoid- and flavonoid-related metabolites were preferentially accumulated in the peripheral cortex rather than in the stele, although the stele constitutes the dominant internal tissue of the tuber. Targeted LC–MS/MS further confirmed that representative hydroxycinnamic acids and caffeoylquinic acid derivatives were enriched in the cortex and, for most validated metabolites, in the cell wall-enriched fraction. Notably, spatial metabolomic profiling also revealed a contrasting stele-biased distribution of indole-related metabolites, including indole-3-acetamide-related features detected by MSI and non-targeted LC–MS and indole-3-acetic acid (IAA) enrichment validated by targeted LC–MS/MS. RT–qPCR analysis showed that phenylpropanoid biosynthetic genes were generally more highly expressed in the cortex and cell wall-enriched fraction, whereas auxin-related genes showed higher expression in the stele. Together, these results show cortex-biased phenylpropanoid accumulation, preferential association of most validated phenylpropanoid-related metabolites with the cell wall-enriched fraction, and stele-associated IAA accumulation and auxin-related transcript expression. This study provides a spatial framework for understanding metabolite partitioning in medicinal aquatic storage organs and highlights the importance of integrating anatomical, metabolomic, and gene expression information in medicinal plant research.

This study reports the isolation and structural characterization of a novel β-fructan (PMP2) from Polygonatum multiflorum using sequential pressing, macroporous resin adsorption, and ultrafiltration (yield: 0.66 %; purity: 93.8 %). Structural analysis revealed a 4.06 kDa polymer with a fructose-dominated composition (Fru/Glu = 86.5:12.9), featuring a linear backbone of →1)-β-D-Fruf-(2→ with →6)-β-D-Fruf-(2→ and →1,6)-β-D-Fruf-(2→ branches, as confirmed by methylation and NMR. SEM revealed lamellar morphology at 400× magnification and porous fibrous structure at 2000×. PMP2 exhibited potent α-amylase inhibition (84.3 % at 0.25 mg/mL) and limited antioxidant activity (e.g., the DPPH scavenging rate was 15.51 ± 1.53 % at 10 mg/mL). Kinetic analysis confirmed competitive inhibition (3.1-fold Km increase; unchanged Vmax), while molecular docking demonstrated high-affinity binding (-17.6 kcal/mol) to the catalytic site through hydrogen bonding and steric blockade. The branching configuration correlates with enhanced enzymatic inhibition, positioning PMP2 as a structurally unique fructan for glycemia-control functional foods. These findings provide foundational data for P. multiflorum utilization.

Euryale ferox (EF), a highly nutritious food, is an excellent source of resistant starch (RS). This study compared the structure, physicochemical properties, and probiotic activities of RS from North (NEFRS) and South EF (SEFRS). NEFRS exhibited a higher RS content (∼10 %) than SEFRS (∼4 %) and demonstrated superior crystallinity (21.66 %), thermal stability (ΔH = 21.85 J/g), and molecular order, whereas SEFRS contained more double helices (ΔH = 4.17 J/g). Both displayed type A crystalline structures, with RS5 amylose-lipid complexes being more abundant in NEFRS during growth. Gas chromatography-mass spectrometry identified bound fatty acids, including palmitic, linoleic, trans-oleic, and stearic acids, confirmed through in vitro synthesis. Probiotic assays revealed EFRS enhanced the growth of Bifidobacterium and Lactobacillus acidophilus, while NEFRS exhibited stronger inhibition against Escherichia coli and Staphylococcus aureus. Overall, this study systematically elucidated the EFRS differences between two species, providing valuable insights into functional product development and EF deep processing.

This study investigates the secondary metabolism regulatory mechanism of the Labiatae medicinal plant Schizonepeta tenuifolia Briq. The monoterpene synthase StLS catalyzes the manufacture of (-)-pulegone, a distinctive monoterpene active component of this species, and its expression level directly impacts secondary metabolite accumulation. Due to the limited knowledge of the StLS transcriptional regulatory network, this study employed a multiomics combined analysis to investigate the role of the R2R3-MYB transcription factor in plant metabolic regulation. It was discovered that StMYB13 and StMYB76 are regulatory elements after a deep analysis of the Arabidopsis thaliana transcriptome database using bioinformatics screening. The yeast one-hybrid system (Y1H) showed that StMYB13/StMYB76 could specifically bind CAACGG in the StLS promoter region from-1,234 to-1,274 bp. Virus-induced gene silencing (VIGS) and transient overexpression were used to unveil the StMYB transcription factor's monoterpene metabolic pathway regulatory network. The transcription factor controlled the monoterpene synthase StLS's transcriptional activity and downstream biosynthetic enzyme-encoding gene expression. The silencing of StMYB genes led to a dramatic reduction (p < 0.001) in the expression of the pivotal gene StIPD, whereas the overexpression system caused a substantial elevation in its mRNA levels. Further analysis demonstrated that this regulatory process exhibits a distinct expression-level-dependent pattern: (-)-pulegone content was significantly elevated in overexpression lines, whereas no statistically significant difference in (-)-pulegone accumulation was observed in silenced groups. These findings revealed StMYBs'transcriptional regulation mechanism and provided molecular evidence for the analysis of S. tenuifolia's volatile oil synthesis nodes. This discovery deepened the monoterpene biosynthesis pathway and laid the theoretical groundwork for metabolic engineering and molecular-assisted breeding systems of S. tenuifolia.

Monoterpenoids are small volatile molecules produced by many plants that have applications in consumer products and healthcare. Plants from the mint family (Lamiaceae) are prodigious producers of monoterpenoids, including a chemotype of Agastache rugosa (Huo Xiang), which produces pulegone and isomenthone. We sequenced, assembled and annotated a haplotype-resolved chromosome-scale genome assembly of A. rugosa with a monoterpene chemotype. This genome assembly revealed that pulegone biosynthesis genes are in a biosynthetic gene cluster, which shares a common origin with the pulegone gene cluster in Schizonepeta tenuifolia. Using phylogenetics and synteny analysis, we describe how the clusters in these two species diverged through inversions and duplications. Using Hi-C analysis, we identified tentative evidence of contact between the pulegone gene cluster and an array of pulegone reductases, with both regions also enriched in retrotransposons. This genome and its analysis add valuable and novel insights to the organization and evolution of terpenoid biosynthesis in Lamiaceae.

ETHNOPHARMACOLOGICAL RELEVANCE:Salvia miltiorrhiza Bunge (Lamiaceae), known as Danshen in China, is a widely utilized traditional Chinese medicine (TCM). Danshen is classified within the heart and liver meridians and renowned for its ability to activate collaterals and blood vessels, facilitate the removal of blood stasis without compromising vital Qi. It plays a pivotal role in promoting blood circulation and alleviating blood stasis. Clinically, it is commonly used to treat uterine bleeding, irregular menstruation, blood stasis, and abdominal pain, among other symptoms. AIM OF THE STUDY:This paper reviews the traditional use, botany, phytochemistry, pharmacology, toxicity, pharmacokinetics and clinical application of Danshen from 1981 to 2024. The goal is to offer valuable reference materials that can inform and guide future research related to Danshen. MATERIALS AND METHODS:A literature search was performed on Danshen based on classic books about Chinese herbal medicine and different electronic databases including Web of Science, PubMed, Elsevier, ScienceDirect, Google Scholar, SciFinder, TPL, and CNKI. RESULTS:Traditional uses of Danshen have been documented in China for centuries. A large number of studies have shown that Danshen is rich in chemical components. To date, more than 318 chemical compounds have been isolated and identified, including diterpenoid quinones, phenolic acids, triterpenes, essential oils, neolignans, alkaloids, flavonoids, saccharides, and others. Crude extracts and pure compounds isolated from Danshen exhibit a wide range of pharmacological effects, including anti-atherosclerotic, anti-arrhythmic, anti-thrombotic, anti-hypertensive, anti-myocardial ischemia-reperfusion injury, endothelial dysfunction protection, sedative and analgesic, neuroprotective, anti-depressive, anti-hepatic fibrosis, anti-pulmonary fibrosis, anti-renal fibrosis, anti-inflammatory, anti-oxidative, anti-tumor, anti-diabetic effects. The results of pharmacokinetic studies showed that the presence of various compounds within the extract of Danshen can significantly influence the pharmacokinetic characteristics of individual constituents through several mechanisms. These mechanisms may include enhanced bioavailability, reduced potential for toxicity, and alterations in the distribution of metabolites. CONCLUSIONS:Danshen has been demonstrated to be a valuable medicinal resource in TCM. This paper provides a comprehensive review of the ethnopharmacology, chemical composition, pharmacological effects, toxicology, pharmacokinetics and clinical applications of Danshen, aiming to serve as a thorough reference for its further development and utilization. Additionally, further research in pharmacokinetics and toxicology is essential to enhance our understanding of its clinical applications and quality control.

Euryales semen (ES, Euryale ferox Salisb.) is a highly nutritious food, which is rich in starch. The quality of ES is usually affected by differences in geographic origin and variety. This study proposed a rapid classification and quantification method based on near-infrared, mid-infrared, and Raman spectroscopy combined with intelligent algorithms to achieve origin traceability and quality evaluation of ES. Traditional chemometrics initially classified ES from different regions and varieties using multispectral data. Machine learning algorithms combined with single and fused datasets were successfully improved the performance of classification models. Random forest (RF) classifier constructed using the feature-level data fusion strategy exhibited optimal performance, with an accuracy of 94.74 % in origin traceability and 100 % in varietal traceability. Moreover, multispectral fingerprints were applied to rapidly determine the contents of total starch in ES. RF regression combined with fused dataset (near-infrared and mid-infrared fingerprints) produced optimal results, with the highest values for the ratio of prediction to deviation and coefficient of determination for prediction of 2.60 and 0.82, respectively. Overall, the proposed combination of multispectral fingerprints with intelligent algorithms shows great potential for origin determination and quality assessment of ES as well as of other foods and herbs.

Euryales Semen (ES, Euryale ferox Salisb.) is a valuable aquatic food in Asia. Its quality and price depend on its geographical origins. To ensure the authenticity of ES, a tracing strategy using stable isotopes, elements, and starch composition with interpretable algorithms was successfully developed. Results indicated that ES from different regions exhibited different chemical fingerprinting profiles. Tree-based intelligent algorithms were introduced for classification, and light gradient boosting machine (LightGBM) achieved the highest accuracy of 97.67%. The SHapley Additive exPlanation (SHAP) interpreted the LightGBM output for feature impact. Notably, the top 10 significant variables, encompassing Na, V, Ba, Sb, Cu, Ti, Mn, %N, amylose, and ratio of amylose to amylopectin (SHAP value >1.0), were selected as the key factors. Moreover, environmental factors were found to be significantly related to these key variables (p < 0.05). Overall, this study offers an effective strategy for the geographical origin traceability of ES or other aquatic crops.

Codonopsis root, a traditional Chinese medicine, produces saccharides that serve as key indicators for assessing its quality. In this study, we employ near-infrared reflectance spectroscopy to predict total polysaccharide concentration as well as the major individual saccharides of intact (surface and cross-section) and ground samples of Codonopsis roots. We developed regression relationships between the spectra and the concentration of fructose, glucose and polysaccharides for the ground spectra set (Rp2 > 0.8, RPD>2.0) based on partial least squares regression (PLSR) model. However, for the intact cross-section spectra set, only the dominant component of the fructose, could be quantitatively detected (Rp2 > 0.8, RPD>2.0). All models based on the intact surface spectra set were of unacceptable performance. This discrepancy could be attributed to the low concentration levels of different saccharides and the distinct chemical profiles reflected by the spectra sets from samples with varying homogeneity. The findings provide an approach for efficient and sustainable analysis for the purposes of quality control and standardization of Codonopsis roots.

Euryales Semen (ES) is a highly nutritious food with low digestibility, which is closely associated with its endogenous phenolic compounds. In this study, five phenolic compounds (naringenin, isoquercitrin, gallic acid, epicatechin and quercetin) with high concentrations in ES were selected to prepare starch-polyphenol complexes. Subsequently, the effects of endogenous polyphenols on the structure, physicochemical properties and digestion characteristics of ES starch were studied using multiple techniques. The addition of phenolic compounds markedly reduced the in vitro digestibility, swelling power, gelatinization enthalpy, while increased the solubility of ES starch. Fourier-transform infrared spectroscopy and X-ray diffraction analysis showed that phenolic compounds interacted with the starch through non-covalent bonds. Five phenolic compounds inhibited α-amylase activity through a mixed competitive inhibition mechanism, with the inhibition potency ranked as follows: quercetin > epicatechin > gallic acid > isoquercitrin > naringenin. The spectroscopic analysis and molecular dynamics simulations confirmed that five phenolic compounds interacted with the amino acid residues of α-amylase through hydrogen bonding and hydrophobic interactions, caused α-amylase static fluorescence quenching, and altered its conformation and microenvironment. This study provides a better understanding of the interaction mechanisms between ES starch and polyphenols, and supports the development of ES as a food that lowers sugar levels.

Perillae Folium (PF) is a well-known food and herb containing different chemotypes, which affect its quality. Herein, a method was proposed to classify and quantify PF chemotypes using gas chromatography-mass spectrometry (GC-MS) and Fourier transform-near infrared spectroscopy (FT-NIR). GC-MS results revealed that PF contains several chemotypes, including perilla ketone (PK) type, α-asarone (PP-as) type, and dillapiole (PP-dm) type, with the PK type being the predominant chemotype. Based on FT-NIR data, different chemotypes were accurately classified. The random forest algorithm achieved >90 % accuracy in chemotype classification. Furthermore, the main components of perilla ketone and isoegomaketone in PF were successfully quantified using partial least squares regression models, with prediction to deviation values of 3.76 and 2.59, respectively. This method provides valuable insights and references for the quality supervision of PF and other foods.

This study investigates the impact of methyl jasmonate (MeJA) on the volatile oil composition of Schizonepeta tenuifolia and elucidates the function of the StTPS45 gene, a key player in terpenoid biosynthesis. The effect of different concentrations of MeJA (0, 50, 100, 200, and 300 μmol/L) on the growth of S. tenuifolia adventitious bud clusters was analyzed over a 20 d period. Using gas chromatography–mass spectrometry (GC-MS), 17 compounds were identified from the adventitious bud clusters of S. tenuifolia. Significant changes in the levels of major monoterpenes, including increased contents of (+)-limonene and (+)-menthone, were observed, particularly at higher concentrations of MeJA. Analysis of transcriptome data from three groups treated with 0, 100, and 300 μmol/L MeJA revealed significant changes in the gene expression profiles following MeJA treatment. At 100 μmol/L MeJA, most terpene synthase (TPS) genes were overexpressed. Additionally, gene expression and functional predictions suggested that StTPS45 acts as germacrene D synthase. Therefore, StTPS45 was cloned and expressed in Escherichia coli, and enzyme activity assays confirmed its function as a germacrene D synthase. Molecular docking and structural prediction of StTPS45 further suggested specific interactions with farnesyl diphosphate (FPP), aligning with its role in the terpenoid synthesis pathway. These findings provide valuable insights into the modulation of secondary metabolite pathways by jasmonate signaling and underscore the potential of genetic engineering approaches to enhance the production of specific terpenoids in medicinal plants.