Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.

Diosgenin, mainly extracted from wild diosgenin-contained Dioscorea species, is a well-known starting material of steroidal and contraceptive drugs. However, due to large market demand and increasingly ecological damage, wild Dioscorea species resources available have been gradually declining. Therefore, identification of new potential ecological distribution of diosgenin-contained Dioscorea species is necessary for diosgenin production. In this study, a large occurrence dataset (1808 data points) of diosgenin-contained Dioscorea species was obtained from Eastern Asia, Southern North America and Southern Africa. Along with the data for six critical environmental parameters and one soil factor, Geographic Information System for Global Medicinal Plant was applied to predict the potential suitable distribution of Dioscorea species. The results showed that the potential distribution of these Dioscorea species covered a wide field, and that new ecological suitability areas were mainly distributed in the central region of South America, the southern part of the European and coastal region of Oceania. Jackknife test indicated that annual precipitation and annual mean radiation were the important climatic factors controlling the distribution of Dioscorea species. The suitable areas and critical climatic factors will serve as a useful guide for diosgenin-contained Dioscorea species conservation and cultivation in ecological suitable areas.

The endangered rate of medicinal plant exceeds that of endangered plant species. However, blindly introducing medicinal plants in regions without comprehensively considering the involved environmental factors results in diseases and insect pests and the consequent overproof pesticide residue as well as reduces the quality of herbal medicine produced. Global Medicinal Plant Geographic Information System (GMPGIS) was developed to analyze environmental information of ecologically suitable regions, thus guiding the conservation and introduction of medicinal plants. This system is based on theories and methods from multiple disciplines, including computer science, geoinformatics, ecology, and traditional herbal medicine. Using a range-based method, the previously established ecologically suitable regions were evaluated. This new method effectively resolved the problem of outlier points, and its functions were implemented in Python. The system automatically calculates the Euclidean distance of climatic factors and intersection of soil factors, thus identifying regions with high ecological similarity and those are climatically and edaphically suitable for the cultivation of medicinal plants. These results, validated using real-world regions, revealed that GMPGIS is highly accurate in screening ecologically suitable regions for the cultivation of medicinal plants worldwide. Overall, because of these features, the GMPGIS is considered as a suitable distribution analysis system for global medicinal plant cultivation.

Based on the gradual transformation from wild growth to artificial cultivation, the accurate authentication of licorice seeds contributes to the first committed step of its quality control and is pivotal to ensure the clinical efficacy of licorice. However, it is still challenging to obtain genetically stable licorice germplasm resources due to the multi-source, multi-heterozygous, polyploid, and hybrid characteristics of licorice seeds. Here, a new method for determining the heterozygosity of licorice seed mixture, based on the various sites, and finding the composition characteristics of licorice seed is preliminarily designed and proposed. Namely, high-throughput full-length multiple DNA barcodes(HFMD), based on ITS multi-copy variation exist, the full-length amplicons of ITS2, psbA-trnH and ITS are directly sequenced by rDNA through the next-generation sequence(NGS) and single-molecule real-time (SMRT) technologies. By comparing the three sequencing methods, our results proved that SMRT sequencing successfully identified the complete gradients of complex mixed samples with the best performance. Meanwhile, HFMD is a brilliant and feasible method for evaluating the heterozygosity of licorice seeds. It shows a perfect interpretation of DNA barcoding and can be applied in multi-base multi-heterozygous and polyploid species.

Introduction: Phyllosphere microorganisms play essential roles in plant health and disease resistance, yet their responses to pathogen infections remain poorly understood. Panax ginseng is susceptible to multiple fungal diseases, which threaten its quality and yield. This study aimed to clarify the underlying disease resistance mechanisms of Panax ginseng by analyzing the phyllosphere fungal communities associated with fungal infections. Methods: Phyllosphere fungal communities of healthy Panax ginseng plants and those with three fungal infections (gray mold, damping-off and root rot) were compared to explore the disease resistance mechanisms related to fungal community changes. Results: Results revealed distinct niche differentiation: leaves were dominated by Basidiomycota (82.0%), while stems harbored more Ascomycota (94.2%), including pathogens like Monilinia laxa (35.73%). Fungal infection significantly reduced microbial alpha diversity, altered community structure (PERMANOVA, p = 0.001), and destabilized co-occurrence networks (modularity decreased from 0.8501 to 0.8116). Functional prediction indicated downregulation of key metabolic pathways (e.g., NAD/NADP interconversion, phospholipid biosynthesis). Disease stress induced an enrichment of potentially beneficial taxa (e.g., Rhodotorula ) in leaves, indicative of a limited antagonistic response, while the overall community was ultimately dominated and disrupted by pathogens. Discussion: Elucidating these compositional shifts of phyllosphere fungal communities advances the understanding of plant–microbe–pathogen interactions and provides a critical theoretical groundwork for development of microbiome-driven early disease diagnosis, resistance breeding, and eco-friendly disease control strategies for Panax ginseng .

Panax ginseng C. A. Mey., a precious traditional medicinal herb, demonstrates diverse pharmacological activities, including immunomodulation and anti-fatigue effects. However, prolonged cultivation has led to germplasm admixture and cultivar degeneration, resulting in inconsistent quality that severely compromises its medicinal value and industrial standardization. Therefore, establishing accurate and efficient germplasm evaluation tools is critical for ensuring the quality of P. ginseng medicinal materials. To integrate whole-genome sequencing and chemical fingerprinting for ginseng germplasm identification and quality consistency assessment. Chromosome-level genomes of ginseng from Jilin (JA) and Liaoning (FC) were assembled using PacBio HiFi, Illumina, and Hi-C technologies. Gene family identification and phylogenetic analysis were performed across 13 representative species. Using the JA genome as the reference, we constructed a pan-genome incorporating 7 ginseng genomes to dissect gene repertoire composition and structural variation distribution across ginseng populations. Population structure analysis with 76 individual ginseng samples revealed genetic diversity, and its integration with HPLC chemical fingerprints provided a joint assessment of quality consistency. We assembled two chromosome-level genomes and, through comparative genomics, revealed significant expansion of ginsenoside biosynthesis-related gene families and subgenome divergence. The core gene set accounted for 54.1% of the pan-genome, indicating high genetic conservation. SNP distribution patterns from population resequencing enabled the development of germplasm-specific molecular markers and a genetic-chemical integrated evaluation model. The molecular marker system and genetic-chemical joint assessment developed here provide reliable novel tools for germplasm identification and quality control, advancing standardization in the ginseng industry.