The Ginseng Genome

Preface to the Series
Preface
Contents
Contributors
Abbreviations
1 Introduction of Panax Ginseng (Origin, Distribution, Germplasm, Cultivation and Economics Importance)
Abstract
1.1 Origin and Evolution of Panax Ginseng
1.1.1 Geological Age of Panax Ginseng Origin
1.1.2 Primitive Area of Panax Ginseng Origin
1.1.3 Intercontinental Disjunction Distribution of Panax Genus
1.1.4 Biological Evolution of Panax Genus
1.1.4.1 Evolution of Panax Genus in Eastern Asia
1.1.4.2 Evolution of Panax Genus in Eastern North America
1.1.5 Polyploidization of Panax Genus
1.2 Distribution of Panax Ginseng
1.2.1 Panax Ginseng Distribution in China
1.2.2 Panax Ginseng Distribution in Korean Peninsula
1.2.3 Panax Ginseng Distribution in Japan
1.2.4 Panax Ginseng Distribution in Russia
1.3 Germplasm Resources of Panax Ginseng
1.3.1 Wild Panax Ginseng Resources
1.3.2 Cultivated Ginseng Resources
1.4 Cultivation of Panax Ginseng
1.4.1 Wild Cultivation Mode
1.4.2 Deforestation Model
1.4.3 Farmland Planting Mode
1.4.4 Comparison of Different Planting Models
1.4.5 Pollution-Free Ginseng Planting Mode
1.5 Economy and World Trade of Panax Ginseng
1.6 Conclusion
References
2 The Ginseng Genome-Traditional Uses, Medicinal Properties, Phytochemistry, and Pharmaceutical Applications
Abstract
2.1 Ginseng in Traditional Medicine and Clinical Uses
2.1.1 Ginseng in Traditional Medicine Concepts and Medicinal Uses
2.1.1.1 Traditional Literatures for Ginseng
2.1.1.2 Medicinal Properties of Ginseng
2.1.1.3 Medicinal Use of Ginseng in Ancient Asian Medicine
2.1.2 Clinical Studies of Ginseng as Drug or Dietary Supplement
2.1.2.1 The Registered Ginseng Clinical Trials
2.1.2.2 The Completed/Published Ginseng Clinical Trials
2.2 Active Components/Chemistry from White and Red Ginseng
2.2.1 Ginsenosides
2.2.2 Polyacetylenes
2.2.3 Polysaccharides
2.3 Pharmaceutical Applications of Ginseng
2.3.1 Memory
2.3.2 Energy
2.3.3 Stress
2.3.4 Antioxidant
2.3.5 Boost the Immune System
References
3 Nucleotide Signature and SNP Double Peak Methods Detect Adulterants and Substitution in Panax Products
Abstract
3.1 Panax ginseng and its Closely Related Species
3.2 Panax ginseng Products and Chinese Patent Medicines
3.3 Identification Methods of Panax Species
3.4 DNA Barcoding and Mini-Barcoding
3.5 Intraspecific Genetic Distances of Medicinal Panax Species
3.6 SNPs Analysis and Double Peak Method Development
3.7 Nucleotide Signature Combined with Double Peak Method Identify Ginseng Chinese Patent Medicines
3.8 A Fast Identification Method of Panax notoginseng Based on Nucleotide Signature and NJ Tree
3.9 Identification of P. notoginseng and Its Related Species and Adulterants
References
4 Breeding of Superior Ginseng Cultivars
Abstract
4.1 Introduction
4.2 Reproduction of Ginseng
4.2.1 Flowering and Reproduction
4.2.2 Seed Harvest and Stratification
4.3 Characteristics of Ginseng Breeding
4.3.1 The Breeding History of Korean Ginseng
4.3.2 Ginseng Breeding Method
4.3.2.1 Pure-Line Selection
4.3.2.2 Crossbreeding
4.3.2.3 Artificial Crossing
4.3.2.4 Breeding and Selection of Superior Inbred Lines
4.3.3 Registration of Novel Ginseng Cultivars
4.4 Characteristics of Major Ginseng Cultivars
4.4.1 Chunpoong
4.4.2 Yunpoong
4.4.3 Gopoong
4.4.4 Sunpoong
4.4.5 Gumpoong
4.4.6 Sunun
4.4.7 Sunwon
4.4.8 Chungsun
4.4.9 Sunhyang
4.4.10 Cheonryang
4.4.11 Gowon
4.5 Conclusion and Perspective
References
5 Molecular Cytogenetics of Panax Ginseng
Abstract
5.1 Introduction
5.2 History of P. ginseng Cytogenetics
5.3 Challenges and Alternative Approaches in Chromosome Preparations
5.4 Repeats in the P. ginseng Genome
5.5 The P. ginseng Karyotype and Chromosome Counts of Related Species
5.6 Repeats Are Drivers for Genome Diversification in Panax Species
5.7 Future Directions in P. ginseng Cytogenetics
References
6 Ginseng Genome and Metabolic Regulation
Abstract
6.1 Introduction
6.2 Characteristics of P. ginseng Genome
6.3 Metabolism and Transcription Characteristics of Ginseng Root
6.4 Conserved Biosynthesis Pathway of Ginsenosides
6.5 Microbial Resistance Genes and HMGR Expression Pattern During Cylindrocarpon Destructans Infection
6.6 The MEP Pathway
6.7 UGTs of P. ginseng
6.8 Transcriptional Factors and Transporters
References
7 Ginseng Genome Structure and Evolution
Abstract
7.1 Introduction
7.2 Genome Size
7.3 Genome Assembly and Annotation
7.4 Genome Duplication
7.5 Phylogenomics of Panax Species
7.6 Evolution History of Ginseng
7.7 Environmental Adaptive Gene Families
7.8 Conclusion and Perspective
References
8 Chloroplast Genome Diversity in Panax Genus
Abstract
8.1 Introduction
8.2 Chloroplast Genome Diversity Among P. Ginseng Accessions
8.3 Phylogenetic Relationship of Panax and Relative Species
8.4 Distribution of Mitochondrial Plastid DNAs (MTPTs) Across the P. Ginseng Chloroplast Genome
8.5 Development of Cp Genome DNA Markers to Authenticate Panax Species
8.6 Conclusion and Perspective
References
9 An Update to the Transcriptome Sequencing for the Genus Panax
Abstract
9.1 Introduction
9.1.1 Panax Ginseng
9.1.2 Panax Notoginseng
9.1.3 Panax Quinquefolius
9.1.4 miRNAs
9.1.5 Other Panax Species
9.2 Conclusion and Perspective
References
10 Metabolic Dynamics and Ginsenoside Biosynthesis
Abstract
10.1 Introduction
10.2 Ginsenoside Biosynthesis-Related Genes
10.2.1 3-Hydroxy-3-Methylglutaryl-CoA Reductase (HMGR)
10.2.2 Mevalonate Diphosphate Decarboxylase (MVD)
10.2.3 Farnesyl Phosphate Synthase (FPS)
10.2.4 Squalene Synthase (SS)
10.2.5 Squalene Epoxidase (SE)
10.2.6 Dammaranediol Synthase (DDS)
10.2.7 β-Amyrin Synthase (β-AS)
10.2.8 Cytochrome P450s
10.2.9 Uridine Diphosphate (UDP)-Glucosyltransferases (UGTs)
10.2.9.1 C-3 Glycosylation
10.2.9.2 C-6 and C-20 Glycosylation
10.3 Physiological Changes of Ginsenoside Accumulation
10.3.1 MeJA Effect on Ginseng UGTs and Ginsenoside Accumulation
10.3.2 UGTs and Ginsenoside Accumulation Regarding Ginseng Development
10.3.3 Effect of Environmental Changes on Ginsenosides Accumulation
10.4 Defense Genes Involved in Biotic and Abiotic Stresses in Ginseng
10.4.1 Catalase (CAT)
10.4.2 Glutathione Peroxidases (GPX)
10.4.3 Glutaredoxin (Grx)
10.4.4 Peroxiredoxin (Prx)
10.4.5 Ascorbate Peroxidase (APX)
10.4.6 Pathogenesis-Related Protein (PRs)
10.4.6.1 PgPR2 (β-Glucanase)
10.4.6.2 PgPR3 (Chitinase)
10.4.6.3 PgPR4
10.4.6.4 PgPR5 (Thaumatin-Like Protein)
10.4.6.5 PgPR6 (Protease Inhibitor)
10.4.6.6 PgPR10 (Ribonuclease)
10.4.7 Lipoxygenase (LOX)
10.5 Defensive Metabolites in Ginseng
10.5.1 Lipid Metabolites
10.5.2 Soluble Sugars and Osmoprotectants
10.5.3 Antioxidants
10.5.4 Secondary Metabolites
10.6 Summary and Conclusions
References
11 Genomic Resources for Ginseng Genome Studies
Abstract
11.1 Introduction
11.2 Gene Annotations
11.3 Download and External Links
11.4 Guidelines for Using Ginseng Genome Database
11.4.1 Search Options
11.4.2 Tools Options
11.5 Conclusion and Perspective
References
12 Genomes of Other Species in Panax Linn
Abstract
12.1 Introduction to Species in Panax Linn
12.2 Sequencing of P. Notoginseng Genome
12.3 Assembly of P. Notoginseng Genome
12.4 Annotation of P. Notoginseng Genome
12.5 Phylogenetic Analysis
12.6 Conclusions and Perspectives
References
13 Synthetic Biology of Ginsenosides
Abstract
13.1 Background
13.1.1 Structural Diversity of Ginsenosides
13.1.2 Traditional Methods of Ginsenoside Production
13.1.3 Advantages of Synthetic Biology as an Alternative Approach to Ginsenoside Production
13.2 Biosynthetic Pathways of Ginsenosides
13.2.1 Biosynthesis of Common Precursors of Triterpenoids
13.2.2 Biosynthesis of Ginsenoside Aglycones
13.2.2.1 Oxidized Squalene Cyclases (OSCs)
13.2.2.2 Cytochromes P450
13.2.2.3 NADPH-Cytochrome P450 Reductase (CPR)
13.2.3 Conversion of Aglycones into Diverse Ginsenosides by UDP-Glycosyltransferases
13.3 Cell Factories Built for Ginsenosides
13.3.1 Cell Factories for Natural Ginsenosides
13.3.1.1 Saccharomyces Cerevisiae
13.3.1.2 Nicotiana Tabacum
13.3.1.3 Oryza Sativa
13.3.1.4 Escherichia Coli
13.3.1.5 Pichia Pastoris
13.3.1.6 Yarrowia Lipolytica
13.3.2 Cell Factories for Non-natural Ginsenosides
13.4 Conclusion and Future Prospects
Acknowledgements
References
14 Gut Microbiome for Ginseng Medicine
Abstract
14.1 Introduction
14.2 Ginsenosides Metabolism Involves Gut Microbiota
14.2.1 20(S)-Protopanaxadiol-Type Ginsenosides (PPD)
14.2.2 20(S)-Protopanaxatriol-Type Ginsenosides (PPT)
14.3 Individual Varied in Ginsenosides Biotransformation
14.4 Improving the Bioavailability of Ginsenosides by Gut Microbiota-Targeted Intervention
14.5 Ginsenosides Biotransformation in Vitro
14.6 Conclusions and Future Perspectives
References