De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments

Transcriptomic strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng

BACKGROUND

Panax ginseng C. A. Meyer, a well-known phytomedicine has been widely used in traditional medicine for centuries. However, its quality and yield are heavily influenced by environmental conditions and cultivation years. For example, ginsenosides as the primary active component of ginseng, the concentration increased with the age of the roots and unevenly distributed across different tissues. Recently, transcriptomic technologies have provided powerful tools for revealing the relationship between gene expression and ginsenoside accumulation during ginseng growth, and researches in this field is continuously expanding, influencing the quality and sustainability of ginseng cultivation.

PURPOSE

Investigating the relationship between ginseng growth and the accumulation of active components may provide new insights for improving ginseng performance and medicinal value. This requires a systematic review and in-depth discussion of relevant research.

STUDY DESIGN AND METHODS

This article reviews the application of transcriptomic strategies in studying the molecular mechanisms of ginseng growth and ginsenoside accumulation. A literature search and analysis were conducted using keywords such as "Panax ginseng" and "transcriptomics/transcriptome," along with terms including "ginsenoside biosynthesis," "microbe/microorganism," "RNA-seq," "cultivation years," "rhizosphere," and "stress."

RESULT

Our study focuses on the transcriptome strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng, we summarized and discussed the dynamic changes in gene expression across cultivation years, specific-tissue, environmental stress, and imbalance of rhizosphere microbes during the ginseng growth and ginsenosides accumulation process. In addition, we also highlight future directions.

CONCLUSION

The cultivation years, specific-tissue, environmental stress, and rhizosphere microbiome imbalance of Panax ginseng are indirectly or directly involved in plant health, biomass production, and the synthesis of ginsenosides. Harnessing these factors to improve the quality and yield of ginseng holds great promise.

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.

Hyperspectral discrimination of ginseng variety and age from Changbai Mountain area

BACKGROUND

The efficacy and market value of Panax ginseng Meyer are significantly influenced by its diversity and age. Traditional identification methods are prone to subjective biases and necessitate the use of destructive sample processing, leading to the loss and wastage of ginseng. Consequently, non-destructive in-situ identification has emerged as a crucial subject of interest for both researchers and the ginseng industry. The advancement of technology and the expansion of research have introduced spectral technology and image processing technology as novel approaches and concepts for non-destructive in-situ identification.

METHODS

Hyperspectral imaging (HSI) is a methodology that combines conventional spectroscopy and imaging to acquire comprehensive spectral and spatial data from various samples. In this study, we investigated the use of Support Vector Machine (SVM) and Spectral Angle Mapper (SAM) classifier algorithms, in conjunction with HSI classification technology, for quasi-Artificial Intelligence (quasi-AI) ginseng identification. To enhance the hyperspectral images prior to SVM classification, we compared the efficacy of Principal Component Analysis (PCA), Minimum Noise Fraction (MNF), and Independent Component Analysis (ICA).

RESULTS

The classification of ginseng based on age was accomplished through the utilization of Radial Basis Function (RBF) kernel SVM and SAM algorithm, which was trained on feature enhanced images. The classification of WMG, MCG, and GG is primarily based on age, with the endmember spectrum serving as the foundation for SAM and SVM.

CONCLUSION

The "endmember spectrum set" derived from the classification outcomes can serve as the "mutation point" for identifying ginseng of different ages.

Mining of disease-resistance genes in Crocus sativus based on transcriptome sequencing

Introduction: Crocus sativus L. has an important medicinal and economic value in traditional perennial Chinese medicine. However, due to its unique growth characteristics, during cultivation it is highly susceptible to disease. The absence of effective resistance genes restricts us to breed new resistant varieties of C. sativus. Methods: In present study, comprehensive transcriptome sequencing was introduced to explore the disease resistance of the candidate gene in healthy and corm rot-infected C. sativus. Results and discussion: Totally, 43.72 Gb of clean data was obtained from the assembly to generate 65,337 unigenes. By comparing the gene expression levels, 7,575 differentially expressed genes (DEGs) were primarily screened. A majority of the DEGs were completely in charge of defense and metabolism, and 152 of them were annotated as pathogen recognition genes (PRGs) based on the PGRdb dataset. The expression of some transcription factors including NAC, MYB, and WRKY members, changed significantly based on the dataset of transcriptome sequencing. Therefore, this study provides us some valuable information for exploring candidate genes involved in the disease resistance in C. sativus.

Effects of growth years on ginsenoside biosynthesis of wild ginseng and cultivated ginseng

BACKGROUND

Ginsenoside, as the main active substance in ginseng, has the function of treating various diseases. However, the ginsenosides content of cultivated ginseng is obviously affected by the growth years, but the molecular mechanism is not clear. In addition, there are significant differences in morphology and physiology between wild ginseng and cultivated ginseng, and the effect of growth years on ginsenoside synthesis not yet understood in wild ginseng.

RESULTS

Transcriptome sequencing on the roots, stems and leaves of cultivated ginseng and wild ginseng with different growth years was performed in this study, exploring the effect of growth years on gene expression in ginseng. The number of differentially expressed genes (DEGs) from comparison groups in cultivated ginseng was higher than that in wild ginseng. The result of weighted gene co-expression network analysis (WGCNA) showed that growth years significantly affected the gene expression of Mitogen-activated protein kinases (MAPK) signaling pathway and terpenoid backbone biosynthesis pathway in cultivated ginseng, but had no effects in wild ginseng. Furthermore, the growth years had significant effects on the genes related to ginsenoside synthesis in cultivated ginseng, and the effects were different in the roots, stems and leaves. However, it had little influence on the expression of genes related to ginsenoside synthesis in wild ginseng. Growth years might affect the expression of genes for ginsenoside synthesis by influencing the expression of these transcription factors (TFs), like my elob lastosis (MYB), NAM, ATAF1 and 2, and CUC2 (NAC), APETALA2/ethylene-responsive factor (AP2/ERF), basic helix-loop-helix (bHLH) and WRKY, etc., thereby affecting the content of ginsenosides.

CONCLUSIONS

This study complemented the gaps in the genetic information of wild ginseng in different growth periods and helped to clarify the potential mechanisms of the effect of growth years on the physiological state in wild ginseng and cultivated ginseng, which also provided a new insight into the mechanism of ginsenoside regulation.

Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis

Background

Ophiocordyceps sinensis is a species endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. Although O. sinensis has been cultivated since the past few years, whether cultivated O. sinensis can completely replace wild O. sinensis remains to be determined.

Methods

To explore the differences of O. sinensis grown in varied environments, we conducted morphological and transcriptomic comparisons between wild and cultivated samples who with the same genetic background.

Results

The results of morphological anatomy showed that there were significant differences between wild and cultivated O. sinensis, which were caused by different growth environments. Then, a total of 9,360 transcripts were identified using Illumina paired-end sequencing. Differential expression analysis revealed that 73.89% differentially expressed genes (DEGs) were upregulated in O. sinensis grown under natural conditions compared with that grown under artificial conditions. Functional enrichment analysis showed that some key DEGs related to fatty acid metabolism, including acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-ketoacyl-CoA thiolase, and acetyl-CoA acetyltransferase, were upregulated in wild O. sinensis. Furthermore, gas chromatography-mass spectrometry results confirmed that the fatty acid content of wild O. sinensis was significantly higher than that of cultivated O. sinensis and that unsaturated fatty acids accounted for a larger proportion.

Conclusion

These results provide a theoretical insight to the molecular regulation mechanism that causes differences between wild and cultivated O. sinensis and improving artificial breeding.

Evaluation of storage period of fresh ginseng for quality improvement of dried and red processed varieties

Background

Dried and red ginseng are well-known types of processed ginseng and are widely used as healthy food. The dried and red ginseng quality may vary with the storage period of raw ginseng. Therefore, herein, the effect of the storage period of fresh ginseng on processed ginseng quality was evaluated through multicomponent quantification with statistical analysis.

Methods

A method based on ultrahigh performance liquid chromatography coupled to triple quadrupole mass spectrometry in multiple-reaction monitoring mode (UPLC-MRM-MS) was developed for quantitation of ginsenosides and oligosaccharides in dried and red ginseng. Principal component analysis and partial least squares discriminant analysis were conducted to evaluate the dynamic distributions of ginsenosides and oligosaccharides after different storage periods.

Results

Eighteen PPD, PPT and OLE ginsenosides and nine reducing and nonreducing oligosaccharides were identified and quantified. With storage period extension, the ginsenoside content in the processed ginseng increased slightly in the first 2 weeks and decreased gradually in the following 9 weeks. The content of reducing oligosaccharides decreased continuously as storage time extending, while that of the nonreducing oligosaccharides increased. Chemical conversions occurred during storage, based on which potential chemical markers for the storage period evaluation of fresh ginseng were screened.

Conclusion

According to ginsenoside and oligosaccharide distributions, it was found that the optimal storage period was 2 weeks and that the storage period of fresh ginseng should not exceed 4 weeks at 0 °C. This study provides deep insights into the quality control of processed ginseng and comprehensive factors for storage of raw ginseng.

Protocol Optimization of Proteomic Analysis of Korean Ginseng (Panax ginseng Meyer)

The benefits of ginseng have been mainly attributed to its triterpenoids, called ginsenosides. Recent genome sequencing of the Panax ginseng has paved the way for in-depth proteomic studies of this medicinal plant. The current study was conducted to deepen the proteomic information on the root proteome of Korean ginseng. Proteomic workflow was optimized by testing two different strategies, characterized by the phenol extraction procedure, the presence or the absence of SDS-PAGE fractionation step, and nano-scale liquid chromatographic tandem mass spectrometry (nLC-MS/MS) analysis. The results highlighted an evident improvement of proteome extraction by the combination of phenol extraction with SDS-PAGE before the nLC-MS/MS analysis. In addition, a dramatic impact of the steaming process (the treatment to produce red ginseng from ginseng) on protein properties was observed. Overall, the analyses of Korean ginseng permitted the characterization of a total of 2412 proteins. A large number of identified proteins belonged to the functional categories of protein and carbon/energy metabolism (22.4% and 14.6%, respectively). The primary and secondary metabolisms are major metabolic pathways, which emerged from the proteomic analysis. In addition, a large number of proteins known to play an important role in response to (a)biotic stresses were also identified. The current proteomic study not only confirmed the previous transcriptomic and proteomic reports but also extended proteomic information, including the main metabolic pathways involved in Korean ginseng.

Development of a Validated UPLC-MS/MS Method for Analyzing Major Ginseng Saponins from Various Ginseng Species

Ginsenosides, which contain one triterpene and one or more sugar moieties, are the major bioactive compounds of ginseng. The aim of this study was to develop and optimize a specific and reliable ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the analysis of twelve different resources of ginseng. The six marker compounds of ginsenoside Rb₁, ginsenoside Rb₂, ginsenoside Rc, ginsenoside Rd, ginsenoside Re, and ginsenoside Rg₁, as well as an internal standard, were separated by a reversed-phase C-18 column with a gradient elution of water and methanol-acetonitrile. The multiple-reaction monitoring (MRM) mode was used to quantify and identify twelve market products. The results demonstrated that not only is the logarithm of its partition coefficient (cLog P; octanol-water partition coefficient) one of the factors, but also the number of sugars, position of sugars, and position of the hydroxyl groups are involved in the complicated separation factors for the analytes in the analytical system. If the amount of ginsenoside Rb₁ was higher than 40 mg/g, then the species might be Panax quinquefolius, based on the results of the marker ginsenoside contents of various varieties. In summary, this study provides a rapid and precise analytical method for identifying the various ginsenosides from different species, geographic environments, and cultivation cultures.

TCMID 2.0: a comprehensive resource for TCM

As a traditional medical intervention in Asia and a complementary and alternative medicine in western countries, Traditional Chinese Medicine (TCM) is capturing worldwide attention in life science field. Traditional Chinese Medicine Integrated Database (TCMID), which was originally launched in 2013, was a comprehensive database aiming at TCM’s modernization and standardization. It has been highly recognized among pharmacologists and scholars in TCM researches. The latest release, TCMID 2.0 (http://www.megabionet.org/tcmid/), replenished the preceding database with 18 203 herbal ingredients, 15 prescriptions, 82 related targets, 1356 drugs, 842 diseases and numerous new connections between them. Considering that chemical changes might take place in decocting process of prescriptions, which may result in new ingredients, new data containing the prescription ingredients was collected in current version. In addition, 778 herbal mass spectrometry (MS) spectra related to 170 herbs were appended to show the variation of herbal quality in different origin and distinguish genuine medicinal materials from common ones while 3895 MS spectra of 729 ingredients were added as the supplementary materials of component identification. With the significant increase of data, TCMID 2.0 will further facilitate TCM’s modernization and enhance the exploration of underlying biological processes that are response to the diverse pharmacologic actions of TCM.

Comparative transcriptome analyses on terpenoids metabolism in field- and mountain-cultivated ginseng roots

BACKGROUND

There exist differences in morphological traits and phytochemical compositions between field- and mountain-cultivated Panax ginseng (FCG and MCG), which might be attributed to variations of terpenoids metabolism adapting to different growth conditions. The present work aims to uncover these variations.

RESULTS

Among 26,648 differentially expressed genes, 496 genes distributed in seven dominant terpenoids pathways were identified. Diterpenoids and triterpenoids biosynthesis genes were significantly higher-expressed in FCG root. Conversely, biosynthesis of carotenoids was significantly more active in MCG root. Additionally, terpenoids backbones, monoterpenoids, sesquiterpenoids, and terpenoid-quinones biosyntheses were neither obviously inclined. Our determination also revealed that there were more gibberellins and steroids accumulated in FCG root which might be responsible for its quick vegetative growth, and enriched abscisic acid and germacrenes as well as protopanaxatriol-type ginsenosides might be major causes of enhanced stress-resistance in MCG root.

CONCLUSIONS

The study firstly provided an overview of terpenoids metabolism in roots of FCG and MCG in elucidating the underlying mechanisms for their different morphological appearances and phytochemical compositions.