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