Phytochemical Genomics: Plant Metabolomics and Medicinal Plant Genomics

Preface
About This Book
Contents
About the Editors
Part I: Introduction to Phytochemicals
	Chapter 1: Phytochemicals: Diversity, Sources and Their Roles
		1 Introduction
		2 Defining Bioactive Phytochemicals
		3 Main Phytochemicals
			3.1 Alkaloids
			3.2 Terpenes
				3.2.1 Monoterpenes
				3.2.2 Sesquiterpenes
				3.2.3 Diterpenoids
				3.2.4 Sesterpenes
				3.2.5 Triterpenes
				3.2.6 Meroterpenes
			3.3 Glycosides
			3.4 Phenolics
		4 Conclusions and Future Directions
		References
	Chapter 2: Phytochemically Rich Medicinally Important Plant Families
		1 Introduction
		2 Extraction of Phytochemicals
		3 Biosynthesis of Phytochemicals
		4 Phytochemically Rich Plant Families and Their Important Biological Activities
			4.1 Amaranthaceae
				4.1.1 Antioxidant Activity
				4.1.2 Anti-inflammatory Activity
				4.1.3 Antiprotozoal Activity
				4.1.4 Anticancer Properties
			4.2 Apiaceae
				4.2.1 Antioxidant Activity
				4.2.2 Anti-inflammatory Activity
				4.2.3 Antimicrobial Activity
			4.3 Cucurbitaceae
				4.3.1 Antioxidant Activity
				4.3.2 Anti-inflammatory Activity
				4.3.3 Anticancer Activity
				4.3.4 Antimicrobial Activity
			4.4 Lamiaceae
				4.4.1 Antioxidant Activity
				4.4.2 Anti-inflammatory Activity
				4.4.3 Antimicrobial Activity
			4.5 Lauraceae
				4.5.1 Antioxidant Activity
				4.5.2 Anti-inflammatory Activity
				4.5.3 Antitumour Activity
		5 Conclusion and Future Perspectives
		References
	Chapter 3: Bioprospecting of Plants for Phytochemicals: Important for Drugs
		1 Introduction
		2 Bioprospecting
			2.1 Chemical Prospecting
			2.2 Gene Prospecting
			2.3 Bionic Prospecting
		3 Computational Approaches for Drug Discovery
		4 Using Evolutionary Tool for Novel Bioactive Compound
		5 Conclusion and Future Prospects
		References
	Chapter 4: Application of Phytochemicals in Therapeutic, Food, Flavor, and Cosmetic Industries
		1 Introduction
		2 Major Groups of Important Phytochemicals
		3 Importance of Phytochemicals in Circular Economy and Sustainability
		4 Applications of Phytochemicals in Various Sectors
			4.1 Phytochemicals in Therapeutics
				4.1.1 Phytochemicals in Cancer Treatment
				4.1.2 Phytochemicals in Cardiovascular Physiology Modification
				4.1.3 Phytochemicals in Diabetes Treatment
				4.1.4 Antimicrobial Properties of Phytochemicals
				4.1.5 Other Therapeutic Applications of Phytochemicals
			4.2 Phytochemicals in Food and Flavor
			4.3 Phytochemicals as Cosmeceuticals
		5 Conclusion and Future Directions
		References
	Chapter 5: Technological Advancements for the Analysis of Phytochemical Diversity in Plants
		1 Introduction
		2 Analysis of Phytochemical Diversity
		3 Technologies Used in Detection and Characterization of Phytochemicals
			3.1 Chromatography
			3.2 Spectroscopy
			3.3 Immunological Techniques
			3.4 Electrochemical Techniques
		4 Major Challenges in Phytochemical Analysis
		5 Conclusion and Future Perspectives
		References
	Chapter 6: Safflower (Carthamus tinctorius) Metabolites and Their Pharmacological Uses
		1 Introduction
		2 Factors Influencing Safflower Cultivation
			2.1 Biotic Stress
			2.2 Abiotic Stress
			2.3 Other Diseases
		3 Omic Approaches
			3.1 Genomics
			3.2 Transcriptomics
			3.3 Metabolomics
		4 Metabolomic Approach in Safflower
		5 Genetic Characteristics Related to the Fatty Acids
			5.1 Flavonoid
			5.2 Other Metabolites
		6 Part-Wise Safflower Pharmacological Compounds and Uses
			6.1 Seed
			6.2 Flower
		7 Pharmacological Importance of Safflower Metabolites
		8 Conclusions
		References
	Chapter 7: A Perspective on Therapeutic Potential of an Invasive Weed, Lantana camara
		1 Introduction
		2 Principal Constituents of Lantana
		3 Pharmacological Activities of Lantana
			3.1 Antibacterial Activity
			3.2 Antifungal Activity
			3.3 Insecticidal Activity
			3.4 Antimalarial Activity
			3.5 Antiulcerogenic Activity
			3.6 Antimycobacterial Activity
			3.7 Wound Healing Activity
			3.8 Antidiarrheal Activity
			3.9 Anticancer and Antiproliferative Activity
			3.10 Antiurolithiatic Activity
			3.11 Antioxidant Activity
			3.12 Antihypertensive Activity
			3.13 Antidiabetic Activity
			3.14 Nephroprotective Activity
			3.15 Toxicological Aspects of Lantana
			3.16 Other Uses of Lantana
		4 Formulations of Lantana
			4.1 Gold Nanoparticles
			4.2 Silver Nanoparticles
			4.3 Cream Formulation
			4.4 Pulsatile Drug Delivery System
		5 Conclusion and Perspectives
		References
	Chapter 8: Algal Phytochemicals from Different Algal Forms with an Emphasis on Genomic Insights into Their Nutraceutical and P...
		1 Introduction
		2 Algal Polysaccharides
			2.1 Algal Polysaccharides as Storage Product
				2.1.1 Starch
				2.1.2 Laminarin
				2.1.3 Floridean Starch
			2.2 Structural Polysaccharides in Algae
				2.2.1 Cellulose
				2.2.2 Alginates
			2.3 Sulfated Polysaccharides
				2.3.1 Agar Agar and Carrageenan
				2.3.2 Furcellaran
				2.3.3 Ulvans
				2.3.4 Spirulans
			2.4 Therapeutic Applications of Algal Polysaccharides
		3 Pigments
			3.1 Phycobilisomes
				3.1.1 Structure and Composition of Phycobilisomes
				3.1.2 Pharmaceutical and Nutraceutical Applications of Phycobilisome and Other Metabolites from Cyanobacteria
			3.2 Carotenoids
				3.2.1 Biosynthesis of Carotenoids
				3.2.2 Application of Carotenoids as Therapeutic Agents
		4 Vitamins
			4.1 Biotin
			4.2 Thiamine
			4.3 Cobalamin
			4.4 Ascorbic Acid
		5 Terpenoids
			5.1 Monoterpenes
			5.2 Diterpenes
			5.3 Triterpenes
			5.4 Sesquiterpenoids
		6 Polyunsaturated Fatty Acids (PUFA)
		7 Application of Biotechnological Tools for Better production of Algal Phytochemicals
		8 Conclusion and Future Perspective
		References
Part II: The Emergence of Phytochemical Omics and Transgenics
	Chapter 9: Emergence of Phytochemical Genomics: Integration of Multi-Omics Approaches for Understanding Genomic Basis of Phyto...
		1 Introduction
		2 Emergence of Phytochemical Genomics
			2.1 Genomics
			2.2 Transcriptomics
			2.3 Proteomics
			2.4 Metabolomics
		3 Employing Genetic Engineering and Gene Editing Tools on the Information Obtained Using Omics Approaches
			3.1 TALENs (Transcription Activator-Like Effector Nucleases)
			3.2 ZFN (Zinc Finger Nucleases)
			3.3 Meganucleases (MN)
			3.4 CRISPR/Cas9
			3.5 Successful Examples of Gene Editing in Medicinal Plants
			3.6 GMO and Gene-Edited Crops
		4 Production of Specialized Metabolites Using Tissue Culture and Hairy Root Culture
		5 Conclusions
		References
	Chapter 10: Application of Transcriptomics in Exploring Important Genes in Medicinal Plants
		1 Introduction
		2 Microarray-Based Identification of Genes Associated Therapeutic Traits
		3 ESTs and EST-Based Markers in Medicinal Plants
		4 Transcriptome Landscape in Medicinal Plants
		5 Role of miRNA in Phytochemical Biosynthesis
		6 Important Genes Involved in the Biosynthesis of Bioactive Compounds
		7 Metabolomics and Transcriptomics
		8 Conclusion and Future Perspectives
		References
	Chapter 11: Metabolomics of Important Medicinal Plants
		1 Introduction
		2 Strategies Employed in Plant Metabolomics
			2.1 Metabolite Profiling
				2.1.1 Nontargeted Approach
				2.1.2 Targeted Approach
			2.2 Metabolite Fingerprinting
			2.3 Metabolite Footprinting
			2.4 Metabonomics
			2.5 Chemoprofiling
			2.6 Metabolic Fluxomics
		3 Technological Advancements in Plant Metabolomics
			3.1 Mass Spectrometry Imaging (MSI)
				3.1.1 Gas Chromatography-Mass Spectrometry (GC-MS)
				3.1.2 Liquid Chromatography-Mass Spectrometry (LC-MS)
				3.1.3 Capillary Electrophoresis-Mass Spectrometry (CE-MS)
			3.2 Nuclear Magnetic Resonance (NMR) Spectroscopy
				3.2.1 2D NMR
				3.2.2 Solid-State NMR
		4 Data Processing Methods
		5 Databases for Handling Metabolomics Data
		6 Applications of Metabolomics in Medicinal Plant Research
			6.1 Investigating the Bioactive Compounds in Medicinal Plants
			6.2 Elucidate the Mode of Action of Herbal Medicine
			6.3 Quality Assessment of Herbal Products
			6.4 Safety and Toxicity Assessment of Natural Products
		7 Conclusions and Future Prospects
		References
	Chapter 12: Metabolomics and Therapeutic Potential of Ophiocordyceps sinensis
		1 Introduction
		2 Metabolomics of Ophiocordyceps sinensis
			2.1 Nucleosides and Their Derivatives
			2.2 Carbohydrates
			2.3 Amino Acids, Polyamines, and Cyclopeptides
			2.4 Fatty Acids, Carboxylic Acids, and Related Compounds
			2.5 Aldehydes, Ketones, Phenol, Pyrazines, and Other Compounds
		3 Therapeutic Potential of Ophiocordyceps sinensis
			3.1 The Antitumor Effects of Ophiocordyceps sinensis
				3.1.1 Breast Cancer
				3.1.2 Hepatocellular Carcinoma
				3.1.3 Lung Cancer
				3.1.4 Oral Cancer
				3.1.5 Murine Leukemia
				3.1.6 Human Bladder Cancer
				3.1.7 Human Colorectal Carcinoma
				3.1.8 Brain Cancer
				3.1.9 Human Liver Cancer
			3.2 Human Gastric Cancer
				3.2.1 Pancreatic Cancer
				3.2.2 Osteogenesis
			3.3 Role of Ophiocordyceps in the Improvement of Kidney Functioning
			3.4 Ophiocordyceps Enhance the Steroidogenesis in Males
			3.5 Immunomodulatory Properties of Ophiocordyceps
			3.6 Hypoglycemic and Hypolipidemic Effects of Ophiocordyceps
			3.7 Anti-inflammatory Roles of Ophiocordyceps
		4 Conclusion and Future Perspective
		References
	Chapter 13: Genomics and Metabolomics: A Strategy for Elucidation of Metabolic Pathways in Medicinal Plants
		1 Introduction
		2 Transcriptomic Analysis in Secondary Metabolism: Advances and Progress
		3 Metabolome Analysis: Tools and Techniques
		4 Secondary Metabolism and Environmental Factors
		5 Metabolomics and Fluxomics: Tools for Metabolite Pathway Engineering
		6 Conclusion
		References
	Chapter 14: Databases Relevant to Phytochemicals and Genes That Govern Biosynthesis of the Phytochemicals
		1 Introduction
		2 Antimicrobial Peptides (AMPs) Databases
		3 Natural Products (NPs) Databases
		4 Medicinal Plants and Essential Oils Databases
		5 Conclusion
		References
	Chapter 15: Trichomics: Trichomes as Natural Chemical Factories
		1 Introduction
		2 Trichomes: Classification and Structure
		3 Development of Trichomes
		4 Biological Functions of Trichomes
			4.1 Abiotic Stress Tolerance
			4.2 Biotic Stress Tolerance
		5 Emergence of Trichomics
		6 Phytochemical Diversity of Trichomes
			6.1 Terpenes
			6.2 Phenolics
			6.3 Methyl Ketones
			6.4 Acyl Sugars
		7 Applications of Phytochemicals from Trichomes
		8 Metabolic Engineering to Convert Trichomes into Natural Chemical Factories
		9 Conclusion and Future Perspectives
		References
	Chapter 16: Transgenic Medicinal Plants for Improved Plant Metabolites Production
		1 Introduction
			1.1 Metabolic Engineering´s Significance in Terms of Excessive Secondary Metabolite Synthesis
			1.2 Transgenic Plants as Biopharma Factories
			1.3 Plant Genetic Engineering Using Nanotechnology
			1.4 Metabolism Modulation by Phyto miRNAs in Medicinal Plants
		2 CRISPR Cas9 in Plants
			2.1 Regulating the Transcription Factor by Advanced Genetic Tools
			2.2 Several Strategies Have the Following Applications in Plant Biotechnology
			2.3 Agricultural Crops Improved through CRISPR/Cas9-Mediated Genetic Engineering
		3 Agrobacterium in Plant Metabolic Engineering Strategies
			3.1 Genetically Modified Plants: Future Perspectives/Directions
			3.2 Modern Pharmacological Research of Artemisia
				3.2.1 Artemisinin from Artemisia
				3.2.2 Sesquiterpenes from Artemisia
				3.2.3 Pros and Cons
		4 Conclusion and Future Perspectives
		References
	Chapter 17: Hairy Root Cultures: A Novel Way to Mass Produce Plant Secondary Metabolites
		1 Introduction
		2 Rhizobium Rhizogenes: Mode of Infection and Transformation
		3 Hairy Roots: Green Factories of Plant Secondary Metabolites
		4 Commercial Scale-Up Process of Hairy Roots
		5 Recent Biotechnological Strategies to Enhance Plant Secondary Metabolites in Hairy Roots
			5.1 Metabolic Engineering
			5.2 Elicitation
		6 Multiple Applications of Hairy Roots
		7 Constraints Encountered with Hairy Root Culturing
		8 Conclusion and Future Prospects
		References
	Chapter 18: Secondary Metabolite Production from Roots/Rhizomes: Prospects and Challenges in Developing Differentiated Culture...
		1 Introduction
		2 Hairy Root Cultures: Advancements and Prospects
			2.1 Factors Influencing HR Formation
			2.2 Enhanced Secondary Metabolite Production through HR Cultures
		3 Adventitious Roots: Induction and Prospects
			3.1 Factors Influencing AR Formation
			3.2 Enhanced Secondary Metabolite Production Through AR Cultures
		4 Applications of AR Culture
		5 Conclusion and Future Perspectives
		References
	Chapter 19: Elicitation: An Efficient Strategy for Enriched Production of Plant Secondary Metabolites
		1 Introduction
		2 Mechanisms of Elicitation and Types of Elicitors
		3 Effect of Biotic Elicitors on Secondary Metabolite Production
			3.1 Carbohydrates and Proteins
			3.2 Rhizobacteria
			3.3 Fungal Cells
			3.4 Hormones
		4 Influence of Abiotic Elicitors on Secondary Metabolite Production
			4.1 Physical Elicitors
			4.2 Chemical Elicitors
			4.3 Nanoelicitation
		5 Concluding Remarks
		References
Part III: Linking Phytochemical Genomics to Gene Editing Tools
	Chapter 20: A Short Review on Genes Regulating Biosynthesis of Major Secondary Metabolites
		1 Introduction
		2 Genetic Regulation of Secondary Metabolite Biosynthesis
			2.1 Genetic Regulation of Biosynthesis of Phenolic Compounds
			2.2 Genetic Regulation of Terpenoids
				2.2.1 Artemisinin
				2.2.2 Taxol
			2.3 Gene Regulation of Nitrogen-Containing Alkaloids
			2.4 Regulation of Sufur-Containing Metabolites (Glucosinolates)
			2.5 Gene Regulation of Other Bioactive Compounds
		3 Conclusions
		References
	Chapter 21: Metabolic Engineering for High-Value Bioactive Compounds from Medicinal Plants
		1 Introduction
		2 Tools of Metabolic Engineering
			2.1 Transcription Factors
			2.2 RNA Interference (RNAi)
			2.3 Enzyme Precursors
		3 Genome-Editing Tools for Improvement of Medicinal Plant Properties
			3.1 Zinc Finger Nucleases (ZFNs)
			3.2 Transcription Activator-Like Effector Nucleases (TALENs)
		4 Genome Engineering in Medicinally Important Plants Using CRISPR/Cas9 Tool
		5 Conclusion and Future Perspectives
		References
	Chapter 22: Applications of Genome Editing Techniques for the Improvement of Medicinal Plants
		1 Introduction
		2 Genome Editing Tools and Their Comparison
			2.1 Meganucleases
			2.2 Oligonucleotide-Directed Mutagenesis (ODM)
			2.3 Zinc Finger Nucleases (ZFNs)
			2.4 Transcription Activator-Like Effector Nucleases (TALENs)
			2.5 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)
			2.6 Comparison of Genome Editing Tools
		3 Application of Genome Editing in Medicinal Plants
			3.1 Camelina sativa
			3.2 Dendrobium officinale
			3.3 Dioscorea zingiberensis
			3.4 Nicotiana tabacum
			3.5 Papaver somniferum
			3.6 Salvia miltiorrhiza
		4 Limitations Associated with Application of Genome Editing Techniques
			4.1 Off-Target Effects
			4.2 Absence of an Efficient Transformation and Regeneration System
			4.3 Challenges with Polyploid Genomes
			4.4 Precise Editing of the Genome
			4.5 Genome-Edited Plants vs. Genetically Modified Organisms
		5 Regulatory Measures for Gene-Edited Plants
		6 Conclusions and Future Perspectives
		References
	Chapter 23: Genome Editing in Medicinal Plants Using CRISPR/Cas9 Tool
		1 Introduction
		2 Importance of Bioactive Compounds in Medicinal Plants and the Effect of Biotic and Abiotic Stress on Secondary Metabolite Pr...
		3 CRISPR/Cas9 Mechanism
		4 Role of CRISPR/Cas9 in the Improvement of Bioactive Pharmaceutical Compound Production
		5 Limitations of CRISPR/Cas9 in Medicinal Plants
		6 Conclusions and Future Perspectives
		References
	Chapter 24: Deciphering the Potential of RNAi Technology as Modulator of Plant Secondary Metabolites with Biomedical Significa...
		1 Introduction
		2 Description and Discovery of RNAi
		3 Components of the Process of RNAi
			3.1 RNA-Induced Silencing Complex (RISC)
			3.2 RNA-Dependent RNA Polymerase (RdRP)
			3.3 Primary and Secondary siRNA
		4 The Mechanism Behind the Actions of RNAi
		5 Applications of RNAi in Medicinal Plants
			5.1 Centella asiatica (L.) Urb. (Apiaceae)
			5.2 Artemisia annua L. (Asteraceae)
			5.3 Panax notoginseng (Burkill) F.H.Chen (Araliaceae)
			5.4 Rehmannia glutinosa (Gaertn.) DC. (Plantaginaceae)
			5.5 Isatis indigotica Fortune ex Lindl. (Brassicaceae)
			5.6 Brassica napus L. (Brassicaceae)
			5.7 Panicum virgatum L. (Poaceae)
			5.8 Papaver somniferum L. (Papaveraceae)
			5.9 Populus sp. (Salicaceae)
			5.10 Betula platyphylla Sukaczev (Betulaceae)
			5.11 Nicotiana tabacum L. (Solanaceae)
		6 Conclusions
		References
	Chapter 25: Regulatory Noncoding RNAs: An Emerging Paradigm for Understanding Phytochemical Biosynthesis and Functioning
		1 Introduction
		2 Regulatory Noncoding RNAs in Plants
		3 miRNA-Mediated Regulation on the Biosynthesis of Secondary Metabolites
		4 Secondary siRNA-Mediated Regulation on the Biosynthesis of Secondary Metabolites
		5 lncRNA-Mediated Regulation on the Biosynthesis of Secondary Metabolites
		6 Using Artificial ncRNAs for Enhanced Plant Phytochemicals
		7 Conclusions and Future Perspectives
		References
Part IV: Applications of Phytochemical Genomics
	Chapter 26: Metabolomics and Genomics for Understanding Stress Biology of Plant Metabolites
		1 Introduction
		2 Metabolomic Approaches
			2.1 Metabolite Profiling
			2.2 Metabolic Fingerprinting
			2.3 Targeted and Untargeted Metabolomics
		3 Stresses and Metabolomics
			3.1 Water and Salinity Stress
			3.2 Temperature Stress
			3.3 Phosphorus and Sulphur Stress
			3.4 Oxidative Stress
		4 Genomic Approaches
			4.1 Salinity and Drought Stress
			4.2 Temperature Stress (Cold and Heat Stress)
			4.3 Metal Stress
			4.4 Microbial Stress
			4.5 Oxidative Stress
		5 Data Analysis
		6 Conclusions
		References
	Chapter 27: DNA Barcoding for the Substantiation of Herbal Products
		1 Introduction
		2 Features of Barcoding Sequences in Plants
		3 Molecular-Based Approaches to DNA Barcoding
		4 Applications of DNA Barcodes and Their Availability
		5 Identification of Medicinal Plants Using DNA Barcode
		6 DNA Barcode Data Availability
		7 DNA Mini-barcode
		8 DNA Barcode Library Worldwide
		9 Barcoding Libraries Generation Overview
		10 Conclusion and Future Prospects
		References
	Chapter 28: Improvements in Taxol Biosynthesis by Metabolic Engineering: Recent Trends
		1 Introduction
		2 Biosynthesis of Taxol
		3 Endophytic Fungi Help in the Biosynthesis of Taxol
		4 Engineered Approaches in E. coli for Improved Taxol Biosynthesis
		5 Conjugation of Porphyrin with Taxol Extracted from Aspergillus flavipes
		6 Metabolic Engineering in Bacillus subtilis for Taxol Biosynthesis
		7 Metabolic Engineering in Taxol Biosynthesis within Yeast Cells
		8 Conclusion
		References
	Chapter 29: Computational Interaction Study of Immunomodulatory Plant Derivatives Against SARS-Cov-2 Mpro Target
		1 Introduction
		2 Different Natural Phytocompounds Used in Ayurvedic Kadha
		3 Molecular Docking
		4 Molecular Dynamics
		5 Materials and Methods
			5.1 Preparation of the Ligand
				5.1.1 ADMET Property
				5.1.2 PASS Program
			5.2 Preparation of Viral Protein
				5.2.1 Ligand Preparation and Analysis of Its Likeliness
				5.2.2 Docking and Analysis
			5.3 Molecular Dynamic Simulation and Analysis
		6 Results
			6.1 Molecular Docking and Analysis of Target Prediction
			6.2 Interaction Studies Between Molecules
			6.3 Prediction of Drug-Likeness Properties
			6.4 Evaluation of ADMET Properties
			6.5 Prediction of Antiviral Activity by Pass Calculation
		7 Molecular Dynamics Simulation and Analysis
		8 Discussion
		9 Conclusion
		References