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Song Y, Zhang Y, Wang X, Yu X, Liao Y, Zhang H, Li L, Wang Y, Liu B, Li W. Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis. HORTICULTURE RESEARCH 2024; 11:uhae107. [PMID: 38883331 PMCID: PMC11179851 DOI: 10.1093/hr/uhae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/31/2024] [Indexed: 06/18/2024]
Abstract
Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside is the most important effective compound within it. Ginseng is an allotetraploid, with complex genetic background, making the study of its metabolic evolution challenging. In this study, we assembled a telomere-to-telomere ginseng reference genome, constructed of 3.45 Gb with 24 chromosomes and 77 266 protein-coding genes. Additionally, the reference genome was divided into two subgenomes, designated as subgenome A and B. Subgenome A contains a larger number of genes, whereas subgenome B has a general expression advantage, suggesting that ginseng subgenomes experienced asymmetric gene loss with biased gene expression. The two subgenomes separated approximately 6.07 million years ago, and subgenome B shows the closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed an expansion of gene families associated with ginsenoside biosynthesis in both ginseng subgenomes. Furthermore, both tandem duplications and proximal duplications play crucial roles in ginsenoside biosynthesis. We also screened functional genes identified in previous research and found that some of these genes located in colinear regions between subgenomes have divergence functions, revealing an unbalanced evolution in both subgenomes and the saponin biosynthesis pathway in ginseng. Our work provides important resources for future genetic studies and breeding programs of ginseng, as well as the biosynthesis of ginsenosides.
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Affiliation(s)
- Yiting Song
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yating Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xikai Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hao Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Songhu Road 2005, Shanghai 200433, China
| | - Yingping Wang
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Dong J, Zhao X, Song X, Wang S, Zhao X, Liang B, Long Y, Xing Z. Identification of Eleutherococcus senticosus NAC transcription factors and their mechanisms in mediating DNA methylation of EsFPS, EsSS, and EsSE promoters to regulate saponin synthesis. BMC Genomics 2024; 25:536. [PMID: 38816704 PMCID: PMC11140872 DOI: 10.1186/s12864-024-10442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND The formation of pharmacologically active components in medicinal plants is significantly impacted by DNA methylation. However, the exact mechanisms through which DNA methylation regulates secondary metabolism remain incompletely understood. Research in model species has demonstrated that DNA methylation at the transcription factor binding site within functional gene promoters can impact the binding of transcription factors to target DNA, subsequently influencing gene expression. These findings suggest that the interaction between transcription factors and target DNA could be a significant mechanism through which DNA methylation regulates secondary metabolism in medicinal plants. RESULTS This research conducted a comprehensive analysis of the NAC family in E. senticosus, encompassing genome-wide characterization and functional analysis. A total of 117 EsNAC genes were identified and phylogenetically divided into 15 subfamilies. Tandem duplications and chromosome segment duplications were found to be the primary replication modes of these genes. Motif 2 was identified as the core conserved motif of the genes, and the cis-acting elements, gene structures, and expression patterns of each EsNAC gene were different. EsJUB1, EsNAC047, EsNAC098, and EsNAC005 were significantly associated with the DNA methylation ratio in E. senticosus. These four genes were located in the nucleus or cytoplasm and exhibited transcriptional self-activation activity. DNA methylation in EsFPS, EsSS, and EsSE promoters significantly reduced their activity. The methyl groups added to cytosine directly hindered the binding of the promoters to EsJUB1, EsNAC047, EsNAC098, and EsNAC005 and altered the expression of EsFPS, EsSS, and EsSE genes, eventually leading to changes in saponin synthesis in E. senticosus. CONCLUSIONS NAC transcription factors that are hindered from binding by methylated DNA are found in E. senticosus. The incapacity of these NACs to bind to the promoter of the methylated saponin synthase gene leads to subsequent alterations in gene expression and saponin synthesis. This research is the initial evidence showcasing the involvement of EsNAC in governing the impact of DNA methylation on saponin production in E. senticosus.
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Affiliation(s)
- Jing Dong
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xuelei Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xin Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shuo Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xueying Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Baoxiang Liang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuehong Long
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Zhaobin Xing
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
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Xiong M, Yang X, Yao L, Li Z, Zhang J, Lv J. Bioassay-guided isolation of three new alkaloids from Suillus bovinus and preliminary mechanism against ginseng root rot. Front Microbiol 2024; 15:1408013. [PMID: 38756729 PMCID: PMC11096550 DOI: 10.3389/fmicb.2024.1408013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
In order to control the occurrence of ginseng root rot caused by Fusarium solani (Mart.) Sacc., the antifungal compounds of the mushroom Suillus bovinus were investigated. And three new alkaloids (1-3), named bovinalkaloid A-C, along with one known analog (4), were isolated and identified by bioassay-guided isolation and spectroscopic analyses. Compound 1 strongly inhibited the mycelial growth and spore germination of F. solani with minimum inhibitory concentration of 2.08 mM. Increases in electrical conductivity, nucleic acid, and protein contents, and decreases in lipid content showed that the membrane permeability and integrity were damaged by compound 1. Compound 1 also increased the contents of malondialdehyde and hydrogen peroxide and the activities of antioxidant enzymes, indicating that lipid peroxidation had taken place in F. solani. Compound 1 may serve as a natural alternative to synthetic fungicides for the control of ginseng root rot.
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Affiliation(s)
- Miaomiao Xiong
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaomin Yang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lan Yao
- Institute of Biology, Hebei Academy of Science, Shijiazhuang, China
| | - Zhuang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jinxiu Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jianhua Lv
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Feng Z, Zheng Y, Jiang Y, Pei J, Huang L. Phylogenetic relationships, selective pressure and molecular markers development of six species in subfamily Polygonoideae based on complete chloroplast genomes. Sci Rep 2024; 14:9783. [PMID: 38684694 PMCID: PMC11059183 DOI: 10.1038/s41598-024-58934-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
The subfamily Polygonoideae encompasses a diverse array of medicinal and horticultural plants that hold significant economic value. However, due to the lack of a robust taxonomy based on phylogenetic relationships, the classification within this family is perplexing, and there is also a scarcity of reports on the chloroplast genomes of many plants falling under this classification. In this study, we conducted a comprehensive analysis by sequencing and characterizing the complete chloroplast genomes of six Polygonoideae plants, namely Pteroxygonum denticulatum, Pleuropterus multiflorus, Pleuropterus ciliinervis, Fallopia aubertii, Fallopia dentatoalata, and Fallopia convolvulus. Our findings revealed that these six plants possess chloroplast genomes with a typical quadripartite structure, averaging 162,931 bp in length. Comparative chloroplast analysis, codon usage analysis, and repetitive sequence analysis demonstrated a high level of conservation within the chloroplast genomes of these plants. Furthermore, phylogenetic analysis unveiled a distinct clade occupied by P. denticulatum, while P. ciliinrvis displayed a closer relationship to the three plants belonging to the Fallopia genus. Selective pressure analysis based on maximum likelihood trees showed that a total of 14 protein-coding genes exhibited positive selection, with psbB and ycf1 having the highest number of positive amino acid sites. Additionally, we identified four molecular markers, namely petN-psbM, psal-ycf4, ycf3-trnS-GGA, and trnL-UAG-ccsA, which exhibit high variability and can be utilized for the identification of these six plants.
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Affiliation(s)
- Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Yuan Jiang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, Sichuan, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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Yu W, Cai S, Zhao J, Hu S, Zang C, Xu J, Hu L. Beyond genome: Advanced omics progress of Panax ginseng. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112022. [PMID: 38311250 DOI: 10.1016/j.plantsci.2024.112022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
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.
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Affiliation(s)
- Wenjing Yu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Siyuan Cai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiali Zhao
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Shuhan Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Chen Zang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China.
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Shi M, Zhang S, Zheng Z, Maoz I, Zhang L, Kai G. Molecular regulation of the key specialized metabolism pathways in medicinal plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:510-531. [PMID: 38441295 DOI: 10.1111/jipb.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
The basis of modern pharmacology is the human ability to exploit the production of specialized metabolites from medical plants, for example, terpenoids, alkaloids, and phenolic acids. However, in most cases, the availability of these valuable compounds is limited by cellular or organelle barriers or spatio-temporal accumulation patterns within different plant tissues. Transcription factors (TFs) regulate biosynthesis of these specialized metabolites by tightly controlling the expression of biosynthetic genes. Cutting-edge technologies and/or combining multiple strategies and approaches have been applied to elucidate the role of TFs. In this review, we focus on recent progress in the transcription regulation mechanism of representative high-value products and describe the transcriptional regulatory network, and future perspectives are discussed, which will help develop high-yield plant resources.
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Affiliation(s)
- Min Shi
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Siwei Zhang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Zizhen Zheng
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Itay Maoz
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon, LeZion, 7505101, Israel
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, 200433, China
| | - Guoyin Kai
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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Luo S, Yang X, Zhang Y, Kuang T, Tang C. Spatial metabolomics method to reveal differential metabolomes in microregions of Panax quinquefolius roots by using ultra-performance liquid chromatography quadrupole/time of flight-mass spectrometry and desorption electrospray ionization mass spectrometry imaging. Food Chem 2024; 435:137504. [PMID: 37813026 DOI: 10.1016/j.foodchem.2023.137504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/11/2023]
Abstract
Panax quinquefolius is a natural homology medicine and food that is rich in bioactive ingredients, such as ginsenosides and polysaccharides. The combination of ultra-performance liquid chromatography quadrupole/time of flight-mass spectrometry (UPLC-Q-TOF/MS) and desorption electrospray ionization mass spectrometry imaging (DESI-MSI) was used for the first time in a spatial metabolomics analysis to comprehensively evaluate the differential components in different microregions of P. quinquefolius. UPLC-Q-TOF/MS and DESI-MSI combined with principal component analysis and orthogonal partial least squares-discriminant analysis were used to screen differential metabolites. UPLC-Q-TOF/MS and DESI-MSI screened 27 and 23 differential metabolites, respectively, among which 15 differential metabolites were identified by both methods. It was found that some components, such as ginsenoside Rg1 and malonyl-ginsenoside Rc, were mainly distributed in P of the transverse slice of P. quinquefolius roots, while ginsenoside Ro and malonyl-ginsenoside Rd were mainly distributed in C. The methods and results of this study could be used to understand the precise localization, biosynthesis, and biological functions of special metabolites in P. quinquefolius.
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Affiliation(s)
- Shiying Luo
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China; School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China
| | - Xuexin Yang
- Waters Technology (Beijing) Co. Ltd., Jinghai Industrial Park, 156 Jinghai 4th Road, Beijing Economic-Technological Development Area, Beijing 100076, China
| | - Yi Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China.
| | - Tingting Kuang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China.
| | - Ce Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China.
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Yuan W, Wang QF, Pei WH, Li SY, Wang TM, Song HP, Teng D, Kang TG, Zhang H. Age-induced Changes in Ginsenoside Accumulation and Primary Metabolic Characteristics of Panax Ginseng in Transplantation Mode. J Ginseng Res 2024; 48:103-111. [PMID: 38223831 PMCID: PMC10785232 DOI: 10.1016/j.jgr.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 01/16/2024] Open
Abstract
Background Ginseng (Panax ginseng Mayer) is an important natural medicine. However, a long culture period and challenging quality control requirements limit its further use. Although artificial cultivation can yield a sustainable medicinal supply, research on the association between the transplantation and chaining of metabolic networks, especially the regulation of ginsenoside biosynthetic pathways, is limited. Methods Herein, we performed Liquid chromatography tandem mass spectrometry based metabolomic measurements to evaluate ginsenoside accumulation and categorise differentially abundant metabolites (DAMs). Transcriptome measurements using an Illumina Platform were then conducted to probe the landscape of genetic alterations in ginseng at various ages in transplantation mode. Using pathway data and crosstalk DAMs obtained by MapMan, we constructed a metabolic profile of transplantation Ginseng. Results Accumulation of active ingredients was not obvious during the first 4 years (in the field), but following transplantation, the ginsenoside content increased significantly from 6-8 years (in the wild). Glycerolipid metabolism and Glycerophospholipid metabolism were the most significant metabolic pathways, as Lipids and lipid-like molecule affected the yield of ginsenosides. Starch and sucrose were the most active metabolic pathways during transplantation Ginseng growth. Conclusion This study expands our understanding of metabolic network features and the accumulation of specific compounds during different growth stages of this perennial herbaceous plant when growing in transplantation mode. The findings provide a basis for selecting the optimal transplanting time.
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Affiliation(s)
- Wei Yuan
- Liaoning University of Traditional Chinese Medicine, China
| | - Qing-feng Wang
- Liaoning University of Traditional Chinese Medicine, China
| | - Wen-han Pei
- Macau University of Science and Technology, China
| | - Si-yu Li
- Liaoning University of Traditional Chinese Medicine, China
| | - Tian-min Wang
- Liaoning University of Traditional Chinese Medicine, China
| | - Hui-peng Song
- Liaoning University of Traditional Chinese Medicine, China
| | | | - Ting-guo Kang
- Liaoning University of Traditional Chinese Medicine, China
| | - Hui Zhang
- Liaoning University of Traditional Chinese Medicine, China
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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2023:elad050. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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Dinday S, Ghosh S. Recent advances in triterpenoid pathway elucidation and engineering. Biotechnol Adv 2023; 68:108214. [PMID: 37478981 DOI: 10.1016/j.biotechadv.2023.108214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.
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Affiliation(s)
- Sandeep Dinday
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Sumit Ghosh
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, Uttar Pradesh, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, Uttar Pradesh, India.
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12
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Ding X, Chen J, Dai C, Shi P, Pan H, Lin Y, Chen Y, Gong L, Chen L, Wu W, Qiu X, Xu J, Huang Z, Liao B. Developing population identification tool based on polymorphism of rDNA for traditional Chinese medicine: Artemisia annua L. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154882. [PMID: 37210961 DOI: 10.1016/j.phymed.2023.154882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Artemisia annua, a well-known traditional Chinese medicine, is the main source for production of artemisinin, an anti-malaria drug. A. annua is distributed globally, with great diversity of morphological characteristics and artemisinin contents. Diverse traits among A. annua populations impeded the stable production of artemisinin, which needs an efficient tool to identify strains and assess population genetic homogeneity. PURPOSE In this study, ribosomal DNA (rDNA), were characterized for A. annua for strains identification and population genetic homogeneity assessment. METHODS The ribosomal RNA (rRNA) genes were identified using cmscan and assembled using rDNA unit of LQ-9 as a reference. rDNA among Asteraceae species were compared performing with 45S rDNA. The rDNA copy number was calculated based on sequencing depth. The polymorphisms of rDNA sequences were identified with bam-readcount, and confirmed by Sanger sequencing and restriction enzyme experiment. The ITS2 amplicon sequencing was used to verify the stability of ITS2 haplotype analysis. RESULTS Different from other Asteraceae species, 45S and 5S linked-type rDNA was only found in Artemisia genus. Rich polymorphisms of copy number and sequence of rDNA were identified in A. annua population. The haplotype composition of internal transcribed spacer 2 (ITS2) region which had moderate sequence polymorphism and relative short size was significantly different among A. annua strains. A population discrimination method was developed based on ITS2 haplotype analysis with high-throughput sequencing. CONCLUSION This study provides comprehensive characteristics of rDNA and suggests that ITS2 haplotype analysis is ideal tool for A. annua strain identification and population genetic homogeneity assessment.
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Affiliation(s)
- Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jieting Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chunyan Dai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peiqi Shi
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hengyu Pan
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yanqi Lin
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yikang Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Linming Chen
- Guangzhou Huibiao Testing Technology Center, Guangzhou 510700, China
| | - Wenguang Wu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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13
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Li M, Ma M, Wu Z, Liang X, Zheng Q, Li D, An T, Wang G. Advances in the biosynthesis and metabolic engineering of rare ginsenosides. Appl Microbiol Biotechnol 2023; 107:3391-3404. [PMID: 37126085 DOI: 10.1007/s00253-023-12549-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Rare ginsenosides are the deglycosylated secondary metabolic derivatives of major ginsenosides, and they are more readily absorbed into the bloodstream and function as active substances. The traditional preparation methods hindered the potential application of these effective components. The continuous elucidation of ginsenoside biosynthesis pathways has rendered the production of rare ginsenosides using synthetic biology techniques effective for their large-scale production. Previously, only the progress in the biosynthesis and biotechnological production of major ginsenosides was highlighted. In this review, we summarized the recent advances in the identification of key enzymes involved in the biosynthetic pathways of rare ginsenosides, especially the glycosyltransferases (GTs). Then the construction of microbial chassis for the production of rare ginsenosides, mainly in Saccharomyces cerevisiae, was presented. In the future, discovery of more GTs and improving their catalytic efficiencies are essential for the metabolic engineering of rare ginsenosides. This review will give more clues and be helpful for the characterization of the biosynthesis and metabolic engineering of rare ginsenosides. KEY POINTS: • The key enzymes involved in the biosynthetic pathways of rare ginsenosides are summarized. • The recent progress in metabolic engineering of rare ginsenosides is presented. • The discovery of glycosyltransferases is essential for the microbial production of rare ginsenosides in the future.
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Affiliation(s)
- Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Mengyu Ma
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
- Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai, 264003, China.
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14
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Ye YN, Liang DF, Yi JH, Jin S, Zeng Z. IGTCM: An integrative genome database of traditional Chinese medicine plants. THE PLANT GENOME 2023:e20317. [PMID: 36896476 DOI: 10.1002/tpg2.20317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Fully understanding traditional Chinese medicines (TCMs) is still challenging because of the extreme complexity of their chemical components and mechanisms of action. The TCM Plant Genome Project aimed to obtain genetic information, determine gene functions, discover regulatory networks of herbal species, and elucidate the molecular mechanisms involved in the disease prevention and treatment, thereby accelerating the modernization of TCMs. A comprehensive database that contains TCM-related information will provide a vital resource. Here, we present an integrative genome database of TCM plants (IGTCM) that contains 14,711,220 records of 83 annotated TCM-related herb genomes, including 3,610,350 genes, 3,534,314 proteins and corresponding coding sequences, and 4,032,242 RNAs, as well as 1033 non-redundant component records for 68 herbs, downloaded and integrated from the GenBank and RefSeq databases. For minimal interconnectivity, each gene, protein, and component was annotated using the eggNOG-mapper tool and Kyoto Encyclopedia of Genes and Genomes database to acquire pathway information and enzyme classifications. These features can be linked across several species and different components. The IGTCM database also provides visualization and sequence similarity search tools for data analyses. These annotated herb genome sequences in IGTCM database are a necessary resource for systematically exploring genes related to the biosynthesis of compounds that have significant medicinal activities and excellent agronomic traits that can be used to improve TCM-related varieties through molecular breeding. It also provides valuable data and tools for future research on drug discovery and the protection and rational use of TCM plant resources. The IGTCM database is freely available at http://yeyn.group:96/.
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Affiliation(s)
- Yuan-Nong Ye
- Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
- Bioinformatics and Biomedical Big Data Mining Laboratory, Department of Medical Informatics, School of Big Health, Guizhou Medical University, Guiyang, China
| | - Ding-Fa Liang
- Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Jia-Hao Yi
- Bioinformatics and Biomedical Big Data Mining Laboratory, Department of Medical Informatics, School of Big Health, Guizhou Medical University, Guiyang, China
| | - Shuai Jin
- Bioinformatics and Biomedical Big Data Mining Laboratory, Department of Medical Informatics, School of Big Health, Guizhou Medical University, Guiyang, China
| | - Zhu Zeng
- Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
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15
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Qiu S, Blank LM. Recent Advances in Yeast Recombinant Biosynthesis of the Triterpenoid Protopanaxadiol and Glycosylated Derivatives Thereof. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2197-2210. [PMID: 36696911 DOI: 10.1021/acs.jafc.2c06888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Plant natural products are a seemingly endless resource for novel chemical structures. However, their extraction often results in high prices, fluctuation in both quantity and quality, and negative environmental impact. The latter might result from the extraction procedure but more often from the high amount of plant biomass required. With the advent of synthetic biology, producing natural plant products in large quantities using yeasts as hosts has become possible. Here, we focus on the recent advances in metabolic engineering of the yeasts species Saccharomyces cerevisiae and Yarrowia lipolytica for the synthesis of ginsenoside triterpenoids, namely, dammarenediol-II, protopanaxadiol, protopanaxatriol, compound K, ginsenoside Rh1, ginsenoside Rh2, ginsenoside Rg3, and ginsenoside F1. A discussion is provided on advanced synthetic biology, bioprocess strategies, and current challenges for the biosynthesis of ginsenoside triterpenoids. Finally, future directions in metabolic and process engineering are summarized and may help reify sustainable ginsenoside production.
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Affiliation(s)
- Shangkun Qiu
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52074 Aachen, Germany
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16
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Ma R, Yang P, Jing C, Fu B, Teng X, Zhao D, Sun L. Comparison of the metabolomic and proteomic profiles associated with triterpene and phytosterol accumulation between wild and cultivated ginseng. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 195:288-299. [PMID: 36652850 DOI: 10.1016/j.plaphy.2023.01.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/02/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Wild ginseng is thought to be superior in its medicinal quality to cultivated ginseng, potentially owing to the differences in active components. This study was designed accordingly to assess the differences in secondary metabolite components and their synthesis in wild and cultivated ginseng by using quantitative proteomics combined with secondary metabolomics approaches. A total of 72 secondary metabolites were found to be differentially abundant, of which dominant abundant in wild ginseng primarily included triterpenoid saponins (ginsenosides) and phytosterols. Ginsenoside diversity was increased in wild ginseng, particularly with respect to rare ginsenosides. Ginsenoside Rk1, F1, Rg5, Rh1, PPT, Rh2, and CK enriched in wild ginseng were validated by HPLC. In addition to ginsenosides, stigmasterol and β-sitosterol were accumulated in wild ginseng. 102 differentially expressed proteins between wild and cultivated ginseng were identified using iTRAQ labeling technique. Among them, 25 were related to secondary metabolism, mainly involved in sesquiterpene and triterpene biosynthesis, which was consistent with metabolomics results. Consistently, the activity levels of HMGR, FDPS, SS, SE, DS, CYP450, GT and CAS, which are key enzymes related to ginsenoside and phytosterol biosynthesis, were confirmed to be elevated in wild ginseng.The biosynthesis of ginsenosides and phytosterols in wild ginseng is higher than that in cultivated ginseng, which may be related to natural growth without artificial domestication. To some extent, this study explained the accumulation of pharmacodynamic components and overall quality of ginseng, which could provide reference for the germplasm improvement and planting of ginseng.
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Affiliation(s)
- Rui Ma
- Research Center of Traditional Chinese Medicine, Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China
| | - Pengdi Yang
- Jilin Technology Innovation Center for Chinese Medicine Biotechnology, Beihua University, 15 Jilin Street, Jilin, Jilin Province, 132013, China
| | - Chenxu Jing
- Research Center of Traditional Chinese Medicine, Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China
| | - Baoyu Fu
- Research Center of Traditional Chinese Medicine, Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China
| | - Xiaoyu Teng
- Jilin Technology Innovation Center for Chinese Medicine Biotechnology, Beihua University, 15 Jilin Street, Jilin, Jilin Province, 132013, China
| | - Daqing Zhao
- Research Center of Traditional Chinese Medicine, Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China; Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China
| | - Liwei Sun
- Research Center of Traditional Chinese Medicine, Affiliated Hospital, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China; Key Laboratory of Active Substances and Biological Mechanisms of Ginseng Efficacy, Ministry of Education, Changchun University of Chinese Medicine, Changchun, Jilin Province, 130021, China.
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17
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Li F, Chen MM, Zhang HM, Wu QP, Han YB. Production of ginsenoside compound K by microbial cell factory using synthetic biology-based strategy: a review. Biotechnol Lett 2023; 45:163-174. [PMID: 36550334 DOI: 10.1007/s10529-022-03326-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/24/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Ginsenoside compound K (CK) is a major intestinal bacterial metabolite of the protopanaxadiol-type ginsenoside family that can be absorbed in the systemic circulation. CK possesses diverse and important pharmacological properties. The low production and high cost of traditional manufacturing methods based on the extraction and biotransformation of total ginsenosides from ginseng have limited their medical application. However, considerable progress has been made in the area of de novo CK production via microbial cell factories using synthetic biology-based strategies. By introducing key enzymes responsible for CK biosynthesis into microbial cells, CK was produced via a series of in vivo enzymatic reactions that utilize the inherent precursors in microbial cells. After systematic optimization using various metabolic engineering strategies, the yield of CK increased significantly and exceeded the traditional plant extraction-biotransformation method, implying the commercial feasibility of this approach. This review summarizes recent novel advancements in the production of CK using microbial cell factories.
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Affiliation(s)
- Feng Li
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Meng Meng Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Hui Min Zhang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qing Ping Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yun Bin Han
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Li L, Lv B, Zang K, Jiang Y, Wang C, Wang Y, Wang K, Zhao M, Chen P, Lei J, Wang Y, Zhang M. Genome-wide identification and systematic analysis of the HD-Zip gene family and its roles in response to pH in Panax ginseng Meyer. BMC PLANT BIOLOGY 2023; 23:30. [PMID: 36639779 PMCID: PMC9838044 DOI: 10.1186/s12870-023-04038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ginseng, Panax ginseng Meyer, is a traditional herb that is immensely valuable both for human health and medicine and for medicinal plant research. The homeodomain leucine zipper (HD-Zip) gene family is a plant-specific transcription factor gene family indispensable in the regulation of plant growth and development and plant response to environmental stresses. RESULTS We identified 117 HD-Zip transcripts from the transcriptome of ginseng cv. Damaya that is widely grown in Jilin, China where approximately 60% of the world's ginseng is produced. These transcripts were positioned to 64 loci in the ginseng genome and the ginseng HD-Zip genes were designated as PgHDZ genes. Identification of 82 and 83 PgHDZ genes from the ginseng acc. IR826 and cv. ChP genomes, respectively, indicated that the PgHDZ gene family consists of approximately 80 PgHDZ genes. Phylogenetic analysis showed that the gene family originated after Angiosperm split from Gymnosperm and before Dicots split from Monocots. The gene family was classified into four subfamilies and has dramatically diverged not only in gene structure and functionality but also in expression characteristics. Nevertheless, co-expression network analysis showed that the activities of the genes in the family remain significantly correlated, suggesting their functional correlation. Five hub PgHDZ genes were identified that might have central functions in ginseng biological processes and four of them were shown to be actively involved in plant response to environmental pH stress in ginseng. CONCLUSIONS The PgHDZ gene family was identified from ginseng and analyzed systematically. Five potential hub genes were identified and four of them were shown to be involved in ginseng response to environmental pH stress. The results provide new insights into the characteristics, diversity, evolution, and functionality of the PgHDZ gene family in ginseng and lay a foundation for comprehensive research of the gene family in plants.
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Affiliation(s)
- Li Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Boxin Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kaiyou Zang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Chaofan Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yanfang Wang
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Ping Chen
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Jun Lei
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Research Center for Ginseng Genetic Resources Development and Utilization, Jilin Province, Jilin Agricultural University, Changchun, Jilin, 130118, China.
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Cheng X, Li X, Liao B, Xu J, Hu L. Improved performance of proteomic characterization for Panax ginseng by strong cation exchange extraction and liquid chromatography-mass spectrometry analysis. J Chromatogr A 2023; 1688:463692. [PMID: 36549145 DOI: 10.1016/j.chroma.2022.463692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Panax ginseng is a precious and ancient medicinal plant. The completion of its genome sequencing has laid the foundation for the study of proteome and peptidome. However, the high abundance of secondary metabolites in ginseng reduces the identification efficiency of proteins and peptides in mass spectrometry. In this report, strong cation exchange pretreatment was carried out to eliminate the interference of impurities. Based on the charge separation of proteolytic peptides and metabolites, the sensitivity of mass spectrometry detection was greatly improved. After pretreatment, 2322 and 2685 proteins were identified from the root and stem leaf extract. Further, the ginseng peptidome was analyzed based on this optimized strategy, where 970 and 653 endogenous peptides were identified from root and stem leaf extract, respectively. Functional analysis of proteins and endogenous peptides provided valuable information on the biological activities, metabolic processes, and ginsenoside biosynthesis pathways of ginseng.
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Affiliation(s)
- Xianhui Cheng
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Xiaoying Li
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China.
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20
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Mohanan P, Yang TJ, Song YH. Genes and Regulatory Mechanisms for Ginsenoside Biosynthesis. JOURNAL OF PLANT BIOLOGY = SINGMUL HAKHOE CHI 2023; 66:87-97. [PMID: 36714200 PMCID: PMC9867542 DOI: 10.1007/s12374-023-09384-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 05/13/2023]
Abstract
Panax ginseng is a medicinal plant belonging to the Araliaceae family. Ginseng is known as the king of oriental medicine, which has been practiced since ancient times in East Asian countries and globally in the modern era. Ginseng is used as an adaptogen, and research shows that it has several pharmacological benefits for various ailments such as cancer, inflammation, diabetes, and neurological symptoms. The pharmacological benefits of ginseng are attributed to the triterpenoid saponin ginsenosides found throughout the Panax ginseng species, which are abundant in its root and are found exclusively in P. ginseng and Panax quinquefolius. Recently, with the completion of the entire ginseng genome sequencing and the construction of the ginseng genome database, it has become possible to access information about many genes newly predicted to be involved in ginsenoside biosynthesis. This review briefly summarizes the current progress in ginseng genome analysis and genes involved in ginsenoside biosynthesis, proposing directions for functional studies of the predicted genes related to ginsenoside production and its regulation.
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Affiliation(s)
- Padmanaban Mohanan
- Plant Genomics and Breeding Research Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
| | - Tae-Jin Yang
- Plant Genomics and Breeding Research Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Department of Agriculture, Forestry and Bioresources, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
| | - Young Hun Song
- Plant Genomics and Breeding Research Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Korea
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Identification of microRNA and analysis of target genes in Panax ginseng. CHINESE HERBAL MEDICINES 2023; 15:69-75. [PMID: 36875435 PMCID: PMC9975625 DOI: 10.1016/j.chmed.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/05/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Objective Ginsenosides, polysaccharides and phenols, the main active ingredients in Panax ginseng, are not different significantly in content between 3 and 5 years old of ginsengs called Yuan ginseng and more than ten years old ones called Shizhu ginseng. The responsible chemical compounds cannot fully explain difference in efficacy between them. According to reports in Lonicerae Japonicae Flos (Jinyinhua in Chinese) and Glycyrrhizae Radix et Rhizoma (Gancao in Chinese), microRNA may play a role in efficacy, so we identified microRNAs in P. ginseng at the different growth years and analyzed their target genes. Methods Using high-throughput sequencing, the RNA-Seq, small RNA-Seq and degradome databases of P. ginseng were constructed. The differentially expressed microRNAs was identified by qRT-PCR. Results A total of 63,875 unigenes and 24,154,579 small RNA clean reads were obtained from the roots of P. ginseng. From these small RNAs, 71 miRNA families were identified by bioinformatics target prediction software, including 34 conserved miRNAs, 37 non-conserved miRNA families, as well as 179 target genes of 17 known miRNAs. Through degradome sequencing and computation, we finally verified 13 targets of eight miRNAs involved in transcription, energy metabolism, biological stress and disease resistance, suggesting the significance of miRNAs in the development of P. ginseng. Consistently, major miRNA targets exhibited tissue specificity and complexity in expression patterns. Conclusion Differential expression microRNAs were found in different growth years of ginsengs (Shizhu ginseng and Yuan ginseng), and the regulatory roles and functional annotations of miRNA targets in P. ginseng need further investigation.
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Xu J, Hu Z, He H, Ou X, Yang Y, Xiao C, Yang C, Li L, Jiang W, Zhou T. Transcriptome analysis reveals that jasmonic acid biosynthesis and signaling is associated with the biosynthesis of asperosaponin VI in Dipsacus asperoides. FRONTIERS IN PLANT SCIENCE 2022; 13:1022075. [PMID: 36798802 PMCID: PMC9928152 DOI: 10.3389/fpls.2022.1022075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/01/2022] [Indexed: 05/27/2023]
Abstract
Dipsacus asperoides is a perennial herb, the roots of which are abundant in asperosaponin VI, which has important medicinal value. However, the molecular mechanism underlying the biosynthesis of asperosaponin VI in D. asperoides remains unclear. In present study, a comprehensive investigation of asperosaponin VI biosynthesis was conducted at the levels of metabolite and transcript during root development. The content of asperosaponin VI was significantly accumulated in two-leaf stage roots, and the spatial distribution of asperosaponin VI was localized in the xylem. The concentration of asperosaponin VI gradually increased in the root with the development process. Transcriptome analysis revealed 3916 unique differentially expressed genes (DEGs) including 146 transcription factors (TFs) during root development in D. asperoides. In addition, α-linolenic acid metabolism, jasmonic acid (JA) biosynthesis, JA signal transduction, sesquiterpenoid and triterpenoid biosynthesis, and terpenoid backbone biosynthesis were prominently enriched. Furthermore, the concentration of JA gradually increased, and genes involved in α-linolenic acid metabolism, JA biosynthesis, and triterpenoid biosynthesis were up-regulated during root development. Moreover, the concentration of asperosaponin VI was increased following methyl jasmonate (MeJA) treatment by activating the expression of genes in the triterpenoid biosynthesis pathway, including acetyl-CoA acetyltransferase (DaAACT), 3-hydroxy-3-methylglutaryl coenzyme A synthase (DaHMGCS), 3-hydroxy-3-methylglutaryl coenzyme-A reductase (DaHMGCR). We speculate that JA biosynthesis and signaling regulates the expression of triterpenoid biosynthetic genes and facilitate the biosynthesis of asperosaponin VI. The results suggest a regulatory network wherein triterpenoids, JA, and TFs co-modulate the biosynthesis of asperosaponin VI in D. asperoides.
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Shi Z, Chen H, Zhou X, Yang W, Lin Y. Pharmacological effects of natural medicine ginsenosides against Alzheimer's disease. Front Pharmacol 2022; 13:952332. [PMID: 36467099 PMCID: PMC9708891 DOI: 10.3389/fphar.2022.952332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/08/2022] [Indexed: 08/04/2023] Open
Abstract
Ginsenosides are the most important pharmacological active ingredient of ginseng, with multiple biological therapeutic targets, mild action and no side effects. It is having shown beneficial effects in vitro and in vivo models of AD. In this review, we analyze large literature, summarize the inhibition of ginsenosides fibrous extracellular deposition of β-amyloid (Aβ) and neurofibrillary tangles (NFTs) of possible mechanisms, and explain the effects of ginsenosides on AD neuroprotection from the aspects of antioxidant, anti-inflammatory, and anti-apoptosis, prove the potential of ginsenosides as a new class of drugs for the treatment of AD. In addition, according to the current clinical application status of natural drugs, this paper analysis the delivery route and delivery mode of ginsenosides from the perspective of pharmacokinetics, providing a deeper insight into the clinical application of ginsenosides in the treatment of AD.
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Affiliation(s)
- Zhikun Shi
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
| | - Hongyu Chen
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
| | - Xu Zhou
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
| | - Wei Yang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
| | - Yang Lin
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
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Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng. Int J Mol Sci 2022; 23:ijms232214016. [PMID: 36430494 PMCID: PMC9698431 DOI: 10.3390/ijms232214016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/06/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression-Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng.
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Li Y, Zhang L, Wang T, Zhang C, Wang R, Zhang D, Xie Y, Zhou N, Wang W, Zhang H, Hu B, Li W, Zhao Q, Wang L, Wu X. The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses. JOURNAL OF PLANT RESEARCH 2022; 135:723-737. [PMID: 36260182 DOI: 10.1007/s10265-022-01417-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
We sequenced and analyzed the complete chloroplast genomes of Lilium amoenum, Lilium souliei, and Nomocharis forrestii in detail, including the first sequence and structural comparison of Nomocharis forrestii. We found that the lengths and nucleotide composition of the three chloroplast genes showed little variation. The chloroplast genomes of the three Lilium species contain 87 protein coding genes (PCGs), 38 tRNAs, and 8 rRNA genes. The only difference is that Nomocharis forrestii had an additional infA pseudogene. In the sequence analysis of the Lilium chloroplast genomes, 216 SSRs, 143 pairs of long repeats, 571 SNPs, and 202 indels were detected. In addition, we identified seven hypervariable regions that can be used as potential molecular markers and DNA barcodes of Lilium through complete sequence alignment. The phylogenetic tree was constructed from the three chloroplast genome sequences of Lilium obtained here and 40 chloroplast genome sequences from the NCBI database (including 35 Lilium species, 4 Fritillaria species, and one species of Smilax). The analysis showed that the species clustering of the genus Lilium essentially conformed to the classical morphological classification system of Comber, but differences in the classification of individual species remained. In our report, we support the reclassification of Lilium henryi and Lilium rosthorniiy in the genus Lilium. In general, this study not only provides genome data for three Lilium species, but also provides a comparative analysis of the Lilium chloroplast genomes. These advances will help to identify Lilium species, clarify the phylogenetic analysis of the Lilium genus, and help to solve and improve the disputes and deficiencies in the traditional morphological classification.
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Affiliation(s)
- Yuan Li
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - LiNa Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - TianXi Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - ChaoChao Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - RuiJia Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - Da Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - YuQi Xie
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - NingNing Zhou
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - WeiZhen Wang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - HuiMin Zhang
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - Bin Hu
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - WenHan Li
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - QingQing Zhao
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China
| | - LiHua Wang
- Flower Research Institute, Yunnan Agriculture Academy of Science, Panlong District, Kunming, 650025, Yunnan, China.
| | - XueWei Wu
- School of Agriculture, Yunnan University, Chenggong District, Kunming, 650091, Yunnan, China.
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DI P, YAN Y, WANG P, YAN M, WANG YP, HUANG LQ. Integrative SMRT sequencing and ginsenoside profiling analysis provide insights into the biosynthesis of ginsenoside in Panax quinquefolium. Chin J Nat Med 2022; 20:614-626. [DOI: 10.1016/s1875-5364(22)60198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/28/2022]
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27
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Liao B, Shen X, Xiang L, Guo S, Chen S, Meng Y, Liang Y, Ding D, Bai J, Zhang D, Czechowski T, Li Y, Yao H, Ma T, Howard C, Sun C, Liu H, Liu J, Pei J, Gao J, Wang J, Qiu X, Huang Z, Li H, Yuan L, Wei J, Graham I, Xu J, Zhang B, Chen S. Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield. MOLECULAR PLANT 2022; 15:1310-1328. [PMID: 35655434 DOI: 10.1016/j.molp.2022.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 03/25/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Artemisia annua is the major natural source of artemisinin, an anti-malarial medicine commonly used worldwide. Here, we present chromosome-level haploid maps for two A. annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production. High-fidelity sequencing, optical mapping, and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A. annua. Approximately 50,000 genes were annotated for each haplotype genome, and a triplication event that occurred approximately 58.12 million years ago was examined for the first time in this species. A total of 3,903,467-5,193,414 variants (SNPs, indels, and structural variants) were identified in the 1.5-Gb genome during pairwise comparison between haplotypes, consistent with the high heterozygosity of this species. Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-diene synthase genes. This correlation was further confirmed by resequencing of 36 A. annua samples with varied artemisinin contents. Circular consensus sequencing of transcripts facilitated the detection of paralog expression. Collectively, our study provides chromosome-level allele-aware genome assemblies for two A. annua strains and new insights into the biosynthesis of artemisinin and its regulation, which will contribute to conquering malaria worldwide.
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Affiliation(s)
- Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shiyu Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ying Meng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yu Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Dandan Ding
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Junqi Bai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Dong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Tomasz Czechowski
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Tingyu Ma
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Caroline Howard
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1RQ, UK
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Haitao Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jiushi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jihai Gao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jigang Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hongyi Li
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ling Yuan
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Ian Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Boli Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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Zhang G, Wei F, Chen Z, Wang Y, Jiao S, Yang J, Chen Y, Liu C, Huang Z, Dong L, Chen S. Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154583. [PMID: 35304141 DOI: 10.1016/j.scitotenv.2022.154583] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co, Ltd., Wenshan 663000, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling 712100, China.
| | - JiaYing Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongzhong Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Congsheng Liu
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Zhixin Huang
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Yang L, Gu Y, Zhou J, Yuan P, Jiang N, Wu Z, Tan X. Whole-Genome Identification and Analysis of Multiple Gene Families Reveal Candidate Genes for Theasaponin Biosynthesis in Camellia oleifera. Int J Mol Sci 2022; 23:ijms23126393. [PMID: 35742835 PMCID: PMC9223445 DOI: 10.3390/ijms23126393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 01/27/2023] Open
Abstract
Camellia oleifera is an economically important oilseed tree. Seed meals of C. oleifera have a long history of use as biocontrol agents in shrimp farming and as cleaning agents in peoples’ daily lives due to the presence of theasaponins, the triterpene saponins from the genus Camellia. To characterize the biosynthetic pathway of theasaponins in C. oleifera, members of gene families involved in triterpenoid biosynthetic pathways were identified and subjected to phylogenetic analysis with corresponding members in Arabidopsis thaliana, Camellia sinensis, Actinidia chinensis, Panax ginseng, and Medicago truncatula. In total, 143 triterpenoid backbone biosynthetic genes, 1169 CYP450s, and 1019 UGTs were identified in C. oleifera. The expression profiles of triterpenoid backbone biosynthetic genes were analyzed in different tissue and seed developmental stages of C. oleifera. The results suggested that MVA is the main pathway for triterpenoid backbone biosynthesis. Moreover, the candidate genes for theasaponin biosynthesis were identified by WGCNA and qRT-PCR analysis; these included 11 CYP450s, 14 UGTs, and eight transcription factors. Our results provide valuable information for further research investigating the biosynthetic and regulatory network of theasaponins.
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Affiliation(s)
- Liying Yang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (L.Y.); (Y.G.); (Z.W.)
| | - Yiyang Gu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (L.Y.); (Y.G.); (Z.W.)
| | - Junqin Zhou
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (L.Y.); (Y.G.); (Z.W.)
- Correspondence: (J.Z.); (X.T.)
| | - Ping Yuan
- Hunan Horticultural Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Nan Jiang
- School of Packing and Material Engineering, Hunan University of Technology, Zhuzhou 412000, China;
| | - Zelong Wu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (L.Y.); (Y.G.); (Z.W.)
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (L.Y.); (Y.G.); (Z.W.)
- Correspondence: (J.Z.); (X.T.)
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Guo HY, Zhang J, Lin LM, Song X, Zhang DD, Cui MH, Long CW, Long YH, Xing ZB. Metabolome and transcriptome analysis of eleutheroside B biosynthesis pathway in Eleutherococcus senticosus. Heliyon 2022; 8:e09665. [PMID: 35706960 PMCID: PMC9190005 DOI: 10.1016/j.heliyon.2022.e09665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/15/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022] Open
Abstract
Eleutheroside B (syringin) is a medicinal active ingredient extracted from Eleutherococcus senticosus (Ruper. et Maxim.) Maxim with high clinical application value. However, its synthesis pathway remains unknown. Here, we analyzed the eleutheroside B biosynthesis pathway in E. senticosus. Consequently, metabolomic and transcriptomic analyses identified 461 differentially expressed genes (DEGs) and 425 metabolites. Further, we identified 7 DEGs and 67 metabolites involved in the eleutheroside B biosynthetic pathway in the eleutheroside B high and low plants. The correlation between the gene and metabolites was explored using the pearson correlation coefficient (PCC) analysis. Caffeoyl-CoA O-methyltransferase, caffeic acid-O-methyltransferase, β-amyrin synthase (β-AS) genes, NAC5, and HB5 transcription factors were identified as candidate genes and transcription factors related to the eleutheroside B synthesis. Eleutheroside B content was the highest at the young stage of the leaves both in the high and low eleutheroside B plants. Quantitative real-time polymerase chain reaction revealed that phenylalanine ammonia-lyase1, cinnamate 4-hydroxylase, β-AS, and leucoanthocyanidin reductase gene had higher expression levels at the young stage of the leaves in the low eleutheroside B plants but lower expression levels in the high eleutheroside B plants. In the present study, we complemented the eleutheroside B biosynthetic pathway by analyzing the expression levels of relevant genes and metabolite accumulation patterns.
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Affiliation(s)
- Hong-Yu Guo
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jie Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Li-Mei Lin
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xin Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Duo-Duo Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Ming-Hui Cui
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
| | | | - Yue-Hong Long
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
- Corresponding author.
| | - Zhao-Bin Xing
- College of Life Sciences, North China University of Science and Technology, Tangshan, China
- Corresponding author.
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Guo S, Liao X, Chen S, Liao B, Guo Y, Cheng R, Xiao S, Hu H, Chen J, Pei J, Chen Y, Xu J, Chen S. A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants. Front Genet 2022; 13:764534. [PMID: 35547259 PMCID: PMC9084321 DOI: 10.3389/fgene.2022.764534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Polygonum is a generalized genus of the Polygonaceae family that includes various herbaceous plants. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Polygonum at the chloroplast (cp) genome-scale level, we sequenced and annotated the complete chloroplast genomes of four Polygonum species using next-generation sequencing technology and CpGAVAS. Then, repeat sequences, IR contractions, and expansion and transformation sites of chloroplast genomes of four Polygonum species were studied, and a phylogenetic tree was built using the chloroplast genomes of Polygonum. The results indicated that the chloroplast genome construction of Polygonum also displayed characteristic four types of results, comparable to the published chloroplast genome of recorded angiosperms. The chloroplast genomes of the four Polygonum plants are highly consistent in genome size (159,015 bp-163,461 bp), number of genes (112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes), gene types, gene order, codon usage, and repeat sequence distribution, which identifies the high preservation among the Polygonum chloroplast genomes. The Polygonum phylogenetic tree was recreated by a full sequence of the chloroplast genome, which illustrates that the P. bistorta, P. orientale, and P. perfoliatum are divided into the same branch, and P. aviculare belongs to Fallopia. The precise system site of lots base parts requires further verification, but the study would provide a basis for developing the available genetic resources and evolutionary relationships of Polygonum.
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Affiliation(s)
- Shuai Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuejiao Liao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shiyu Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiming Guo
- Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ruiyang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haoyu Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Chen
- Beijing Engineering Research Center of Pediatric Surgery, Engineering and Transformation Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yangjin Chen
- Department of City and Regional Planning, Nanjing University, Nanjing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Fang X, Wang M, Zhou X, Wang H, Wang H, Xiao H. Effects of growth years on ginsenoside biosynthesis of wild ginseng and cultivated ginseng. BMC Genomics 2022; 23:325. [PMID: 35461216 PMCID: PMC9035264 DOI: 10.1186/s12864-022-08570-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/19/2022] [Indexed: 11/15/2022] Open
Abstract
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08570-0.
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Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng). Arch Microbiol 2022; 204:208. [PMID: 35275265 DOI: 10.1007/s00203-022-02815-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023]
Abstract
Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.
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Meng F, Tang Q, Chu T, Li X, Lin Y, Song X, Chen W. TCMPG: an integrative database for traditional Chinese medicine plant genomes. HORTICULTURE RESEARCH 2022; 9:uhac060. [PMID: 35591924 PMCID: PMC9113410 DOI: 10.1093/hr/uhac060] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/25/2022] [Indexed: 05/12/2023]
Abstract
Because of their great therapeutic and economic value, medicinal plants have attracted increasing scientific attention. With the rapid development of high-throughput sequencing technology, the genomes of many medicinal plants have been sequenced. Storing and analyzing the increasing volume of genomic data has become an urgent task. To solve this challenge, we have proposed the Traditional Chinese Medicine Plant Genome database (TCMPG, http://cbcb.cdutcm.edu.cn/TCMPG/), an integrative database for storing the scattered genomes of medicinal plants. TCMPG currently includes 160 medicinal plants, 195 corresponding genomes, and 255 herbal medicines. Detailed information on plant species, genomes, and herbal medicines is also integrated into TCMPG. Popular genomic analysis tools are embedded in TCMPG to facilitate the systematic analysis of medicinal plants. These include BLAST for identifying orthologs from different plants, SSR Finder for identifying simple sequence repeats, JBrowse for browsing genomes, Synteny Viewer for displaying syntenic blocks between two genomes, and HmmSearch for identifying protein domains. TCMPG will be continuously updated by integrating new data and tools for comparative and functional genomic analysis.
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Affiliation(s)
- Fanbo Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiang Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianzhe Chu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xianhai Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yue Lin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
- Corresponding authors. E-mail: ,
| | - Wei Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
- Corresponding authors. E-mail: ,
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Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias. SCIENCE CHINA. LIFE SCIENCES 2022; 65:809-817. [PMID: 34378141 PMCID: PMC8354779 DOI: 10.1007/s11427-021-1968-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However, the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database (GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias (Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People's Republic of China, and U.S. Pharmacopoeia's Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://www.gpgenome.com and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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Zhang Y, Chen Q, Huang Y, Zhao R, Sun J, Yuan X, Xu H, Liu H, Wu Y. Gene excavation and expression analysis of CYP and UGT related to the post modifying stage of gypenoside biosynthesis in Gynostemma pentaphyllum (Thunb.) Makino by comprehensive analysis of RNA and proteome sequencing. PLoS One 2021; 16:e0260027. [PMID: 34874937 PMCID: PMC8651138 DOI: 10.1371/journal.pone.0260027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
Previous studies have revealed that gypenosides produced from Gynostemma pentaphyllum (Thunb.) Makino are mainly dammarane-type triterpenoid saponins with diverse structures and important biological activities, but the mechanism of diversity for gypenoside biosynthesis is still unclear. In this study, a combination of isobaric tags for relative and absolute quantification (iTRAQ) proteome analysis and RNA sequencing transcriptome analysis was performed to identify the proteins and genes related to gypenoside biosynthesis. A total of 3925 proteins were identified by proteomic sequencing, of which 2537 were quantified. Seventeen cytochrome P450 (CYP) and 11 uridine 5’-diphospho-glucuronosyltransferase (UDP-glucuronosyltransferase, UGT) candidate genes involved in the side chain synthesis and modification of gypenosides were found. Seven putative CYPs (CYP71B19, CYP77A3, CYP86A7, CYP86A8, CYP89A2, CYP90A1, CYP94A1) and five putative UGTs (UGT73B4, UGT76B1, UGT74F2, UGT91C1 and UGT91A1) were selected as candidate structural modifiers of triterpenoid saponins, which were cloned for gene expression analysis. Comprehensive analysis of RNA sequencing and proteome sequencing showed that some CYPs and UGTs were found at both the transcription and translation levels. In this study, an expression analysis of 7 CYPs and 5 UGTs that contributed to gypenoside biosynthesis and distribution in G. pentaphyllum was performed, providing consistent results that will inspire more future research on vital genes/proteins involved in gypenoside biosynthesis.
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Affiliation(s)
- Yangmei Zhang
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
- Department of Nursing, Sichuan Nursing Vocational College, Sichuan province, China
| | - Qicong Chen
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
- School of Biomedical Science and Engineering, South China University of Technology, Guangzhou, Guangdong province, China
| | - Yuanheng Huang
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
| | - Ruiqiang Zhao
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
| | - Jian Sun
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
| | - Xidong Yuan
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
| | - Huiming Xu
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
| | - Huiyu Liu
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
| | - Yaosheng Wu
- Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi province, China
- * E-mail:
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Chen Y, Wu J, Yu D, Du X. Advances in steroidal saponins biosynthesis. PLANTA 2021; 254:91. [PMID: 34617240 DOI: 10.1007/s00425-021-03732-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
This work reviews recent advances in the pathways and key enzymes of steroidal saponins biosynthesis and sets the foundation for the biotechnological production of these useful compounds through transformation of microorganisms. Steroidal saponins, due to their specific chemical structures and active effects, have long been important natural products and that are irreplaceable in hormone production and other pharmaceutical industries. This article comprehensively reviewed the previous and current research progress and summarized the biosynthesis pathways and key biosynthetic enzymes of steroidal saponins that have been discovered in plants and microoganisms. On the basis of the general biosynthetic pathway in plants, it was found that the starting components, intermediates and catalysing enzymes were diverse between plants and microorganisms; however, the functions of their related enzymes tended to be similar. The biosynthesis pathways of steroidal saponins in microorganisms and marine organisms have not been revealed as clearly as those in plants and need further investigation. The elucidation of biosynthetic pathways and key enzymes is essential for understanding the synthetic mechanisms of these compounds and provides researchers with important information to further develop and implement the massive production of steroidal saponins by biotechnological approaches and methodologies.
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Affiliation(s)
- Yiyang Chen
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Junkai Wu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Dan Yu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Xiaowei Du
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China.
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Tien NQD, Ma X, Man LQ, Chi DTK, Huy NX, Nhut DT, Rombauts S, Ut T, Loc NH. De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng ( Panax vietnamensis Ha et Grushv.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2215-2229. [PMID: 34744362 PMCID: PMC8526660 DOI: 10.1007/s12298-021-01076-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 05/04/2023]
Abstract
UNLABELLED Vietnamese ginseng (Panax vietnamensis Ha et Grushv.), also known as Ngoc Linh ginseng, is a high-value herb in Vietnam. Vietnamese ginseng has been proven to be effective in enhancing the immune system, human memory, anti-stress, anti-inflammatory, anti-cancer, and prevent aging. The present study reports the first draft whole-genome of Vietnamese ginseng and the identification of potential genes involved in the triterpenoid metabolic pathway. De novo whole-genome assembly was performed successfully from a data of approximately 139 Gbps of 394,802,120 high quality reads to generate 9815 scaffolds with an N50 value of 572,722 bp from the leaf of Vietnamese ginseng. The assembled genome of Vietnamese ginseng is 3,001,967,204 bp long containing 79,374 gene models. Among them, there are 55,012 genes (69.30%) were annotated by various public molecular biology databases. The potential genes involved in triterpenoid saponin biosynthesis in Vietnamese ginseng and their metabolic pathway were also predicted." Three genes encoding squalene monooxygenase isozymes in Vietnamese ginseng were cloned, sequenced and characterized. Moreover, expression levels of several key genes involved in terpenoid biosynthesis in different parts of Vietnamese ginseng were also analyzed. The SSR markers were detected by various programs from both of assembly full dataset of Vietnamese ginseng genome and predicted genes. The present work provided important data of the draft whole-genome of Vietnamese ginseng for further studies to understand the role of genes involved in ginsenoside biosynthesis and their metabolic pathway at the molecular level of this rare medicinal species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01076-1.
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Affiliation(s)
- Nguyen Quang Duc Tien
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
- Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Xiao Ma
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
| | - Le Quang Man
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Duong Thi Kim Chi
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | | | - Duong-Tan Nhut
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Dalat, 670000 Vietnam
| | - Stephane Rombauts
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
| | - Tran Ut
- Ngoc Linh Ginseng and Medicinal Materials Development Center, Quang Nam Quang Ngai, 51000 Vietnam
| | - Nguyen Hoang Loc
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
- Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
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Huang D, Ming R, Xu S, Wang J, Yao S, Li L, Huang R, Tan Y. Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis. DNA Res 2021; 28:6367775. [PMID: 34499150 PMCID: PMC8476931 DOI: 10.1093/dnares/dsab018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/06/2021] [Indexed: 01/16/2023] Open
Abstract
Gynostemma pentaphyllum (Thunb.) Makino is an economically valuable medicinal plant belonging to the Cucurbitaceae family that produces the bioactive compound gypenoside. Despite several transcriptomes having been generated for G. pentaphyllum, a reference genome is still unavailable, which has limited the understanding of the gypenoside biosynthesis and regulatory mechanism. Here, we report a high-quality G. pentaphyllum genome with a total length of 582 Mb comprising 1,232 contigs and a scaffold N50 of 50.78 Mb. The G. pentaphyllum genome comprised 59.14% repetitive sequences and 25,285 protein-coding genes. Comparative genome analysis revealed that G. pentaphyllum was related to Siraitia grosvenorii, with an estimated divergence time dating to the Paleogene (∼48 million years ago). By combining transcriptome data from seven tissues, we reconstructed the gypenoside biosynthetic pathway and potential regulatory network using tissue-specific gene co-expression network analysis. Four UDP-glucuronosyltransferases (UGTs), belonging to the UGT85 subfamily and forming a gene cluster, were involved in catalyzing glycosylation in leaf-specific gypenoside biosynthesis. Furthermore, candidate biosynthetic genes and transcription factors involved in the gypenoside regulatory network were identified. The genetic information obtained in this study provides insights into gypenoside biosynthesis and lays the foundation for further exploration of the gypenoside regulatory mechanism.
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Affiliation(s)
- Ding Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.,Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Ruhong Ming
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaochang Yao
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.,Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Liangbo Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Rongshao Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Yong Tan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.,Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine, Guangxi University of Chinese Medicine, Nanning 530200, China
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Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng. Int J Mol Sci 2021; 22:ijms22168694. [PMID: 34445398 PMCID: PMC8395461 DOI: 10.3390/ijms22168694] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots; however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.
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Zhou GR, Liao BS, Li QS, Xu J, Chen SL. Establishing a genomic database for the medicinal plants in the Brazilian Pharmacopoeia. Chin Med 2021; 16:71. [PMID: 34353338 PMCID: PMC8340495 DOI: 10.1186/s13020-021-00484-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/29/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Brazil is exceptionally abundant in medicinal plant resources and has a rich ethnopharmacological history. Brazilian Pharmacopoeia (BP) acts as a national standard that regulates drug quality and has six published editions. Recent genomic approaches have led to a resurgence of interest in herbal drugs. The genomic data of plants has been used for pharmaceutical applications, protecting natural resources, and efficiently regulating the market. However, there are few genomic databases specifically for medicinal plants, and the establishment of a database that focuses on the herbs contained in the BP is urgently required. METHODS The medicinal plant species included in each edition of the BP were analyzed to understand the evolution of the Brazilian herbal drugs. The data of 82 plants in the BP were collected and categorized into four sections: DNA barcodes, super-barcodes, genomes, and sequencing data. A typical web server architecture pattern was used to build the database and website. Furthermore, the cp-Gs of the Aloe genus in the database were analyzed as an illustration. RESULTS A new database, the Brazilian Pharmacopoeia Genomic Database (BPGD) was constructed and is now publicly accessible. A BLAST server for species identification and sequence searching with the internal transcribed spacer 2 (ITS2), the intergenic region (psbA-trnH), and the chloroplast genome (cp-G) of Brazilian medicinal plants was also embedded in the BPGD. The database has 753 ITS2 of 76 species, 553 psbA-trnH and 190 genomes (whole genome and chloroplast genome) of 57 species. In addition, it contains 37 genome sequence data sets of 24 species and 616 transcriptome sequence data sets of 34 species and also includes 187 cp-Gs representing 57 medicinal species in the BP. Analyses of the six cp-Gs of three Aloe species identified the variable regions in the cp-Gs. These can be used to identify species and understand the intraspecific relationships. CONCLUSIONS This study presents the first genomic database of medicinal plants listed in the latest BP. It serves as an efficient platform to obtain and analyze genomic data, accelerate studies regarding Brazilian medicinal plants and facilitate the rational development on their market regulation.
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Affiliation(s)
- Guan-Ru Zhou
- Institute of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430000, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Bao-Sheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qiu-Shi Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shi-Lin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Xiao S, Chu Y, Chen Y, Zhao Q, Liao B, Zhang J, Gao Y, Xu J, Chen S. Genome-wide identification and transcriptional profiling analysis of PIN/PILS auxin transporter gene families in Panax ginseng. CHINESE HERBAL MEDICINES 2021; 14:48-57. [PMID: 36120122 PMCID: PMC9476816 DOI: 10.1016/j.chmed.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/12/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yang Chu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yanjun Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qinghe Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yuan Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Corresponding author.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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Chopra P, Chhillar H, Kim YJ, Jo IH, Kim ST, Gupta R. Phytochemistry of ginsenosides: Recent advancements and emerging roles. Crit Rev Food Sci Nutr 2021; 63:613-640. [PMID: 34278879 DOI: 10.1080/10408398.2021.1952159] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ginsenosides, a group of tetracyclic saponins, accounts for the nutraceutical and pharmaceutical relevance of the ginseng (Panax sp.) herb. Owing to the associated therapeutic potential of ginsenosides, their demand has been increased significantly in the last two decades. However, a slow growth cycle, low seed production, and long generation time of ginseng have created a gap between the demand and supply of ginsenosides. The biosynthesis of ginsenosides involves an intricate network of pathways with multiple oxidation and glycosylation reactions. However, the exact functions of some of the associated genes/proteins are still not completely deciphered. Moreover, ginsenoside estimation and extraction using analytical techniques are not feasible with high efficiency. The present review is a step forward in recapitulating the comprehensive aspects of ginsenosides including their distribution, structural diversity, biotransformation, and functional attributes in both plants and animals including humans. Moreover, ginsenoside biosynthesis in the potential plant sources and their metabolism in the human body along with major regulators and stimulators affecting ginsenoside biosynthesis have also been discussed. Furthermore, this review consolidates biotechnological interventions to enhance the biosynthesis of ginsenosides in their potential sources and advancements in the development of synthetic biosystems for efficient ginsenoside biosynthesis to meet their rising industrial demands.
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Affiliation(s)
- Priyanka Chopra
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Himanshu Chhillar
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Ick Hyun Jo
- Department of Herbal Crop Research, Rural Development Administration, Eumseong, South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, College of Natural Resources and Life Sciences, Pusan National University, Miryang, South Korea
| | - Ravi Gupta
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India.,Department of Forestry, Environment, and Systems, College of Science and Technology, Kookmin University, Seoul, South Korea
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45
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Chen Z, Li J, Hou N, Zhang Y, Qiao Y. TCM-Blast for traditional Chinese medicine genome alignment with integrated resources. BMC PLANT BIOLOGY 2021; 21:339. [PMID: 34273956 PMCID: PMC8285853 DOI: 10.1186/s12870-021-03096-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
The traditional Chinese medicine (TCM) genome project aims to reveal the genetic information and regulatory network of herbal medicines, and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Moreover, the TCM genome could provide the basis for the discovery of the functional genes of active ingredients in TCM, and for the breeding and improvement of TCM. The traditional Chinese Medicine Basic Local Alignment Search Tool (TCM-Blast) is a web interface for TCM protein and DNA sequence similarity searches. It contains approximately 40G of genome data on TCMs, including protein and DNA sequence for 36 TCMs with high medical value.The development of a publicly accessible TCM genome alignment database hosted on the TCM-Blast website ( http://viroblast.pungentdb.org.cn/TCM-Blast/viroblast.php ) has expanded to query multiple sequence databases to obtain TCM genome data, and provide user-friendly output for easy analysis and browsing of BLAST results. The genome sequencing of TCMs helps to elucidate the biosynthetic pathways of important secondary metabolites and provides an essential resource for gene discovery studies and molecular breeding. The TCMs genome provides a valuable resource for the investigation of novel bioactive compounds and drugs from these TCMs under the guidance of TCM clinical practice. Our database could be expanded to other TCMs after the determination of their genome data.
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Affiliation(s)
- Zhao Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Jing Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Ning Hou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Yanling Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
| | - Yanjiang Qiao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
- Research Center of TCM-Information Engineering, State Administration of Traditional Chinese Medicine of The Peoples Republic of China, Yangguang South Avenue, Fangshan District, Beijing, 102488 China
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Hou M, Wang R, Zhao S, Wang Z. Ginsenosides in Panax genus and their biosynthesis. Acta Pharm Sin B 2021; 11:1813-1834. [PMID: 34386322 PMCID: PMC8343117 DOI: 10.1016/j.apsb.2020.12.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Ginsenosides are a series of glycosylated triterpenoids which belong to protopanaxadiol (PPD)-, protopanaxatriol (PPT)-, ocotillol (OCT)- and oleanane (OA)-type saponins known as active compounds of Panax genus. They are accumulated in plant roots, stems, leaves, and flowers. The content and composition of ginsenosides are varied in different ginseng species, and in different parts of a certain plant. In this review, we summarized the representative saponins structures, their distributions and the contents in nearly 20 Panax species, and updated the biosynthetic pathways of ginsenosides focusing on enzymes responsible for structural diversified ginsenoside biosynthesis. We also emphasized the transcription factors in ginsenoside biosynthesis and non-coding RNAs in the growth of Panax genus plants, and highlighted the current three major biotechnological applications for ginsenosides production. This review covered advances in the past four decades, providing more clues for chemical discrimination and assessment on certain ginseng plants, new perspectives for rational evaluation and utilization of ginseng resource, and potential strategies for production of specific ginsenosides.
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Key Words
- ABA, abscisic acid
- ADP, adenosine diphosphate
- AtCPR (ATR), Arabidopsis thaliana cytochrome P450 reductase
- BARS, baruol synthase
- Biosynthetic pathway
- Biotechnological approach
- CAS, cycloartenol synthase
- CDP, cytidine diphosphate
- CPQ, cucurbitadienol synthase
- CYP, cytochrome P450
- DDS, dammarenediol synthase
- DM, dammarenediol-II
- DMAPP, dimethylallyl diphosphate
- FPP, farnesyl pyrophosphate
- FPPS (FPS), farnesyl diphosphate synthase
- GDP, guanosine diphosphate
- Ginsenoside
- HEJA, 2-hydroxyethyl jasmonate
- HMGR, HMG-CoA reductase
- IPP, isopentenyl diphosphate
- ITS, internal transcribed spacer
- JA, jasmonic acid
- JA-Ile, (+)-7-iso-jasmonoyl-l-isoleucine
- JAR, JA-amino acid synthetase
- JAZ, jasmonate ZIM-domain
- KcMS, Kandelia candel multifunctional triterpene synthases
- LAS, lanosterol synthase
- LUP, lupeol synthase
- MEP, methylerythritol phosphate
- MVA, mevalonate
- MVD, mevalonate diphosphate decarboxylase
- MeJA, methyl jasmonate
- NDP, nucleotide diphosphate
- Non-coding RNAs
- OA, oleanane or oleanic acid
- OAS, oleanolic acid synthase
- OCT, ocotillol
- OSC, oxidosqualene cyclase
- PPD, protopanaxadiol
- PPDS, PPD synthase
- PPT, protopanaxatriol
- PPTS, PPT synthase
- Panax species
- RNAi, RNA interference
- SA, salicylic acid
- SE (SQE), squalene epoxidase
- SPL, squamosa promoter-binding protein-like
- SS (SQS), squalene synthase
- SUS, sucrose synthase
- TDP, thymine diphosphate
- Transcription factors
- UDP, uridine diphosphate
- UGPase, UDP-glucose pyrophosphosphprylase
- UGT, UDP-dependent glycosyltransferase
- WGD, whole genome duplication
- α-AS, α-amyrin synthase
- β-AS, β-amyrin synthase
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Affiliation(s)
- Maoqi Hou
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Rufeng Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Su X, Xue Q, Sun M, Liu J, Wong MH, Wang C, Chen S. Co-production of polysaccharides, ginsenosides and succinic acid from Panax ginseng residue: A typical industrial herbal waste. BIORESOURCE TECHNOLOGY 2021; 331:125073. [PMID: 33819907 DOI: 10.1016/j.biortech.2021.125073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Co-production of polysaccharides, ginsenosides and succinic acid was achieved from Panax ginseng residue (PGR) in this study. Physico-chemical separation was first applied to recover the released polysaccharides and ginsenoside. Enzymatic hydrolysis was then conducted to covert the left PGR into mono-sugars which was following transformed into succinic acid by constructing a succinic acid-producing strain of Escherichia coli-ZW333. Results indicated that the yields of polysaccharides and ginsenosides increased according to the increase of deconstruction content of PGR. A total sugar yield reached 52 g/L at 10% PGR loading and increased to 94.33 g/L following fed-batch enzymatic hydrolysis. Finally, 56.28 g/L succinic acid was produced. In total, 18 g ginseng polysaccharides, 230 mg ginsenosides and 39 g succinic acid were produced from 100 g PGR. Accordingly, the total economic output could reach RMB 80,149 from 1 t PGR, illustrating the great value increasement of PGR by this industrially possible process.
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Affiliation(s)
- Xinyao Su
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, PR China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301607, PR China
| | - Qiang Xue
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, PR China
| | - Mengchu Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, PR China
| | - Jiarou Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, PR China; College of Bioscience and Bioengineering, Hebei University of Science & Technology, Shijiazhuang 050000, PR China
| | - Ming Hung Wong
- Consortium on Health, Environment, Education and Research (CHEER), and Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, PR China
| | - Caixia Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, PR China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, PR China
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Hongmei S, Wenrui H, Dianyun H, Yang X. Complete chloroplast genome sequence of Dendranthema zawadskii Herbich. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2117-2119. [PMID: 34250234 PMCID: PMC8245063 DOI: 10.1080/23802359.2021.1942261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dendranthema zawadskii Herbich is one of 17 species of Dendranthema in China, and it is often used as an ornamental plant. The chloroplast genome size of Dendranthema zawadskii Herbich is 150,995 bp, including a large single-copy region (82,771 bp), a small single-copy region (18,308 bp), and a pair of inverted repeats regions (24,958 bp). Total 112 genes were annotated, including 79 protein-coding genes, four ribosomal RNA genes, and 29 transfer RNA genes. The phylogenetic position of Dendranthema zawadskii Herbich is close to Dendranthema indicum.
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Affiliation(s)
- Sun Hongmei
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,Infinitus (China) Co. Ltd., Jiangmen, China
| | - He Wenrui
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hou Dianyun
- Agricultural College, Henan University of Science and Technology, Luoyang, China
| | - Xiuwei Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicine, School of Pharmaceutical Science, Peking University, Beijing, China
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49
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Song Z, Li X. Recent Advances in Molecular Marker-Assisted Breeding for Quality Improvement of Traditional Chinese Medicine. Curr Pharm Biotechnol 2021; 22:867-875. [PMID: 32351179 DOI: 10.2174/1389201021666200430121013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The quality of Traditional Chinese Medicine (TCM), reflected by its bioactive compounds and associated contents, is directly linked to its clinical efficacy. Therefore, it is of great importance to improve the quality of TCM by increasing the bioactive compound content. METHODS Mapping the active component content-associated QTLs in TCM and further markerassisted breeding has enabled us to rapidly and effectively cultivate new varieties with high bioactive compound contents, which has opened the door for genetic breeding studies on medicinal plants. RESULTS In this paper, a strategy and technical molecular breeding method for TCM are discussed. The development of four methods and progress in functional marker development, as well as the applications of such markers in TCM, are reviewed. CONCLUSION The progress in, challenges of, and future of marker-assisted breeding for quality improvement of TCM are discussed, which provide valuable scientific references for future molecular breeding.
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Affiliation(s)
- Zhenqiao Song
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
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50
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Yin X, Hu H, Shen X, Li X, Pei J, Xu J. Ginseng Omics for Ginsenoside Biosynthesis. Curr Pharm Biotechnol 2021; 22:570-578. [PMID: 32767915 DOI: 10.2174/1389201021666200807113723] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/09/2020] [Accepted: 06/01/2020] [Indexed: 11/22/2022]
Abstract
Ginseng, also known as the king of herbs, has been regarded as an important traditional medicine for several millennia. Ginsenosides, a group of triterpenoid saponins, have been characterized as bioactive compounds of ginseng. The complexity of ginsenosides hindered ginseng research and development both in cultivation and clinical research. Therefore, deciphering the ginsenoside biosynthesis pathway has been a focus of interest for researchers worldwide. The new emergence of biological research tools consisting of omics and bioinformatic tools or computational biology tools are the research trend in the new century. Ginseng is one of the main subjects analyzed using these new quantification tools, including tools of genomics, transcriptomics, and proteomics. Here, we review the current progress of ginseng omics research and provide results for the ginsenoside biosynthesis pathway. Organization and expression of the entire pathway, including the upstream MVA pathway, the cyclization of ginsenoside precursors, and the glycosylation process, are illustrated. Regulatory gene families such as transcriptional factors and transporters are also discussed in this review.
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Affiliation(s)
- Xianmei Yin
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Chengdu 611137, China
| | - Haoyu Hu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaofeng Shen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiangyan Li
- Changchun University of Traditional Chinese Medicine, Changchun 13000, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Key Laboratory of Distinctive Chinese Medicine Resources in Southwest China, Chengdu 611137, China
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institution of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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