Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae)

Development of a leaf metabolite-based intact sample distinguishing algorithm for the three varieties of Panax Vietnamensis

Panax vietnamensis, indigenous to Vietnam and southern China, is classified into three subspecies: Panax vietnamensis Ha et Grushv. (PVV), Panax vietnamensis var. fuscidiscus (PVF), and Panax vietnamensis var. langbianensis (PVL). A method to distinguish these varieties in their intact form is absent, which poses a possible risk of misclassification. Here, we aimed to devise a plant metabolite-based discrimination algorithm for the three varieties, without causing significant damage to individual plants. A multivariate analysis on mass spectral data of PVV, PVF, and PVL revealed that a peak at m/z 426, which was subsequently identified as an indole alkaloid glycoside, was exclusive to PVF and therefore clearly distinguished PVF from PVV and PVL. Additionally, global metabolic profiling was conducted to elucidate the discrimination markers between PVV and PVL, and lysophospholipids and hydroxy fatty acids were selected as potential discrimination markers. The performance of these markers was validated by cross-validation using machine learning algorithm.

Ethnopharmacology, genetic diversity, phytochemistry and pharmacological effects of Panax vietnamensis Ha et Grushv.: A review

Ginseng is considered as a beneficial herbal remedy and over recent years its efficacy and safety have been verified in clinical therapy. There are two typical species of ginseng including Asian and American ginseng. The varieties of both species have been applied for commercialized materials in different stages of processing from raw to processed products. Panax vietnamensis Ha et Grushv. (P. vietnamensis) belongs to Asian ginseng and has been utilized as effective herbal remedy. P. vietnamensis is believed to improve immune response, longevity and consequent health. There are more than 300 bioactive compounds have been isolated from P. vietnamensis and classified in various groups, such as ginsenosides, flavonoids, phenolics.... These biological activities consist of anti-tumor, anti-inflammatory, neu-roprotective and anti-stress, which are validated by in vitro and in vivo studies. In this review, we systematize the literatures about ethnopharmacology, major bioactive constituents, and toxicology of P. vietnamensis, which were certified by various studies. Furthermore, we also summarize the current method to micro-propagate and lists of extracting sources of bioactive compounds (root, leave, stem.) and the solvents deployed during extraction process. Therefore, this review would provide the firm-evidences and premise for the therapeutic potentials of P. vietnamensis in the future.

Phytochemistry, quality control and biosynthesis in ginseng research from 2021 to 2023: A state-of-the-art review concerning advances and challenges

Panax L. (Araliaceae) has a long history of medicinal and edible use due to its significant tonifying effects, and ginseng research has been a hot topic in natural products research and food science. In continuation of our recent ginseng review, we highlighted the advances in ginseng research from 2021 to 2023 with 157 citations, which exhibited the increasingly systematic, collaborative, and intelligent characteristics. In this review, we firstly updated the progress in phytochemistry involving the ginsenosides and polysaccharides and summarized the researches on the active components. Then, some specific applications by feat of the multidimensional chromatography, mass spectrometry imaging, DNA barcoding, and metabolomics, were analyzed, which could provide rich information supporting the multi-component characterization, authentication, and quality control of ginseng and the versatile products. Finally, the recent biosynthesis studies concerning ginsenosides were retrospected. Additionally, the current challenges and future trends with respect to ginseng research were discussed.

A First Approach for the In Vitro Cultivation, Storage, and DNA Barcoding of the Endangered Endemic Species Euonymus koopmannii

Euonymus koopmannii is a rare and protected species in Kazakhstan, valued for its ecological role in soil stabilization and its ornamental properties. This study presents the first use of micropropagation and phylogenetic analysis for the endemic plant E. koopmannii. Seedlings of E. koopmannii proved to be more effective than internodes as primary explants for plant micropropagation of in vitro culture, with a multiplication coefficient of 28.5 from seedlings and 6.1 from internodes. On MSR I medium supplemented with 0.5 mg/L IBA and 0.05 mg/L IAA, a higher success rate of 67% was achieved for root formation of test tube-grown E. koopmannii plants. Using mannitol as an osmotic agent at a concentration of 8 mg/L prolonged the storage time of E. koopmannii under slow growth conditions when compared to CCC and abscisic acid. Phylogenetic relationships and species identification were analyzed using four DNA-barcoding markers, comparing E. koopmannii with species from NCBI. All candidate barcoding markers showed sufficient levels of interspecific genetic variation among Euonymus species. In addition, ITS region and rbcL gene sequences effectively distinguished E. koopmannii from other species. These results provide fundamental information that will be valuable for future biotechnological and molecular studies.

Beyond genome: Advanced omics progress of Panax ginseng

Ginseng is a perennial herb of the genus Panax in the family Araliaceae as one of the most important traditional medicine. Genomic studies of ginseng assist in the systematic discovery of genes related to bioactive ginsenosides biosynthesis and resistance to stress, which are of great significance in the conservation of genetic resources and variety improvement. The transcriptome reflects the difference and consistency of gene expression, and transcriptomics studies of ginseng assist in screening ginseng differentially expressed genes to further explore the powerful gene source of ginseng. Protein is the ultimate bearer of ginseng life activities, and proteomic studies of ginseng assist in exploring the biosynthesis and regulation of secondary metabolites like ginsenosides and the molecular mechanism of ginseng adversity adaptation at the overall level. In this review, we summarize the current status of ginseng research in genomics, transcriptomics and proteomics, respectively. We also discuss and look forward to the development of ginseng genome allele mapping, ginseng spatiotemporal, single-cell transcriptome, as well as ginseng post-translational modification proteome. We hope that this review will contribute to the in-depth study of ginseng and provide a reference for future analysis of ginseng from a systems biology perspective.

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.

Untargeted Metabolomics Approach for the Differentiation between Panax vietnamensis var. vietnamensis and Panax vietnamensis var. fuscidiscus

Panax vietnamensis var. vietnamensis (PVV) and Panax vietnamensis var. fuscidiscus (PVF) both belong to Panax vietnamensis species and are chemically and morphologically similar, making it hard to distinguish for the consumer. Herein, 42 PVF and 12 PVV samples were collected in Quang Nam and Lai Chau Province, respectively, and subsequently characterized by ITSr-DNA sequence data to verify their origins. Next, untargeted metabolomics combined with multivariate statistical analysis was developed to differentiate PVV and PVF. The metabolic profiles of PVV and PVF were found to be distinct and classified well using Partial Least-Squares Discriminant Analysis (PLS-DA) in the training set. Among them, seven ginsenosides were of high abundance in PVV, while six were of high abundance in PVF. Next, the test set was used to validate 13 putative differential markers found in the training set, illustrating a complete match with the expression patterns of these ginsenosides in the training set. Finally, PLS-DA and linear Support Vector Machine models both indicated distinct ginsenoside profiles of PVV and PVF without misclassification in the test set. Conclusively, the developed untargeted metabolomics approach might serve as a powerful tool for the authentication of PVV and PVF at the metabolome level.