Molecular Genetics and Genomics Tools in Biodiversity Conservation

Foreword
Preface
Contents
About the Editors
1: Phylogenetics and its Application in Biodiversity Conservation
1.1 What Is a Phylogenetic Tree?
1.2 Ways to Reconstruct Phylogenetic Trees
1.2.1 Different Types of Data
1.2.2 Different Methods to Reconstruct a Phylogenetic Tree
1.2.2.1 Distance Methods
1.2.2.2 Maximum Parsimony (MP), Maximum Likelihood (ML), and Bayesian Methods
1.2.3 Time-Calibrated Phylogenetic Trees
1.3 Application of Phylogenetics in Biodiversity Conservation
1.3.1 Application of Phylogenetics in Conservation Planning
1.3.2 Application of Phylogenetics in Wildlife Forensics
1.3.3 The Value of Phylogenetic Diversity in Biodiversity Conservation
1.4 Summary
References
2: Phylogenetics in the Context of Tree Diversity and Conservation
2.1 Introduction
2.2 Molecular Phylogenetics for Biodiversity Conservation
2.3 Common Methods Used in Construction of a Phylogenetic Tree
2.4 Applications of phylogenetics
2.5 Future Perspectives of Phylogenetics into Biodiversity Conservation
References
3: Conservation Metagenomics: Understanding Microbiomes for Biodiversity Sustenance and Conservation
3.1 Introduction
3.2 Genomics and its Applications: Past, Present, and Future
3.3 Microbial Genomics and Metagenomics
3.4 Conservation Metagenomics
3.5 Anthropological Effects on Microbiota Composition
3.6 Strategies and Applications of Metagenomics
3.7 Metagenomics: Sequencing Technology and Analysis Tools
3.8 Applications in Biodiversity Conservation
3.9 Conclusion
References
4: Overview of Omics-Assisted Techniques for Biodiversity Conservation
4.1 Introduction
4.2 Genomics-Assisted Species Conservation
4.3 Transcriptomics-Assisted Species Conservation
4.4 Proteogenomics-Assisted Species Conservation
4.5 Metabolomics-Assisted Species Conservation
4.6 Conclusion
References
5: Genetic Consequences of Fragmentation in Tropical Forests: Novel Approaches to Assess and Monitor Critically Endangered Spe...
5.1 Introduction
5.2 Impacts of Forest Fragmentation and Habitat Loss on Species Demography and Fitness
5.3 Impacts of Forest Fragmentation on Genetic Diversity and Evolutionary Processes
5.4 Methods to Assess Fragmentation Impacts on Genetic Diversity
5.4.1 Measuring Gene Flow Via Paternity Analysis and Seed Dispersal Patterns
5.4.2 Estimating Inbreeding Depression
5.4.3 Test for a Fine-Scale Genetic Structure (FSGS) among Populations
5.5 Empirical Pieces of Evidence for Genetic and Evolutionary Consequences from Tropics
5.6 Novel Tools and Methods to Conserve Genetic Resources
5.6.1 Measuring Adaptive Potential
5.6.2 Simulating Genetic Data to Design Process-Based Conservation Plans
5.6.3 Common Challenges
5.7 Summary and Conclusions
References
6: Molecular Markers in Assessing Genetic Clonal Fidelity for in Vitro Propagated Endangered Medicinal Plants
6.1 Introduction
6.2 Somaclonal Variation in Plant Tissue Culture
6.3 Molecular Markers in Clonal Fidelity Assessment
6.3.1 Restriction Fragment Length Polymorphism (RFLP)
6.3.2 Random Amplified Polymorphic DNA (RAPD)
6.3.3 Amplified Fragment Length Polymorphism (AFLP)
6.3.4 Inter-Simple Sequence Repeat (ISSR)
6.3.5 Start Codon Targeted (SCoT)
6.3.6 Inter-Retrotransposon Amplified Polymorphism (IRAP)
6.3.7 Sequence-Related Amplified Polymorphism (SRAP)
6.3.8 Sequence-Specific Amplification Polymorphism (SSAP)
6.4 Discussion and Conclusions
References
7: Strategies, Opportunities, and Challenges in Crop Genetic Diversity Conservation: A Plant Breeder´s Perspective
7.1 Introduction
7.2 Are Crop Genetic Diversity and Plant Breeding Mutually Exclusive?
7.3 Strategies of Crop Genetic Diversity Conservation
7.3.1 Germplasm Collection
7.3.2 Germplasm Conservation
7.3.2.1 Molecular Strategies of Plant Genetic Resources´ Conservation
7.3.2.2 Genotyping by Sequencing (GBS)
7.3.2.3 NGS and High-Throughput SNP Profiling of Genetic Resources in Crop Plants Using Genotyping Arrays
7.3.2.4 Association Mapping for the Conservation of Plant Genetic Resources
7.3.3 Core Collection for Plant Genetic Resource Conservation, Characterization, and Utilization
7.4 Opportunities in Crop Genetic Diversity Conservation
7.4.1 Germplasm Identification
7.4.2 Germplasm Characterization to Identify Source of Material for Climate Change Adaptation
7.4.3 Pre-Breeding of Valuable PGRs
7.4.4 Fear-Free Germplasm Exchange in Gene Banks
7.5 Challenges in Crop Genetic Diversity Conservation
References
8: Soil Microbial Metagenomics in Agroforestry System: Tools and Techniques
8.1 Introduction
8.2 Amplicon/Marker Sequencing (Metataxonomics)
8.3 Shotgun Metagenomics
8.3.1 Experimental Design
8.3.2 Sample Collection and Nucleic Acid Extraction
8.3.3 Library Preparation and Sequencing
8.3.4 Computational Analysis
8.4 Conclusion
References
9: Molecular Phylogeny of Citrus species in the Eastern Himalayan Region of Northeast India Based on Chloroplast and Nuclear D...
9.1 Introduction
9.2 Materials and Methods
9.2.1 Taxon Sampling
9.2.2 DNA Extraction, Amplification, and Sequencing
9.2.3 Sequence Alignment and Analysis
9.2.4 Phylogenetic Analyses
9.2.4.1 Parsimony Analysis
9.2.4.2 Maximum Likelihood Analysis
9.2.4.3 Bayesian Analysis
9.3 Results
9.3.1 Phylogenetic Analyses
9.4 Discussion
9.5 Conclusion
References
10: Next-Generation Amplicon Sequencing: A Cost-Effective Method for Exploring Microbial Biodiversity
10.1 Microbial Biodiversity
10.2 Exploring the Unseen Majority
10.3 Amplicon Sequencing
10.3.1 Sampling and Library Generation
10.3.1.1 Sample Collection
10.3.1.2 DNA Extraction
10.3.1.3 Primer Selection and Variable Regions
10.3.1.4 PCR Amplification and Multiplexing
10.3.1.5 Sequencing
10.4 Bioinformatic Workflow
10.4.1 Quality Filtering and Chimeric Sequence Removal
10.4.2 Resolving OTUs/ASVs
10.4.3 Taxonomic Annotation
10.4.4 Normalization and Correcting for Gene Copy Number
10.4.5 Multiple Sequence Alignment and Phylogeny Construction
10.4.6 Diversity Analysis
10.5 Conclusion
References
11: Molecular Characterization and Phylogeny of Clerodendrum Species Occuring in North Eastern Region of India by Internal Tra...
11.1 Introduction
11.2 Materials and Methodology
11.2.1 Field Survey and Sample Collection
11.2.2 Molecular Characterization and Identification
11.2.2.1 Isolation of Genomic DNA by Modified CTAB Protocol
11.2.2.2 PCR Amplification of Genomic DNA
11.2.2.3 Quantification of PCR Products and Sequencing
11.2.2.4 DNA Sequence Analysis and Construction of Phylogeny
11.3 Results
11.3.1 Internal Transcribed Spacer (ITS) Sequence Characteristics
11.3.2 BLAST Analysis of ITS2 Sequences Clerodendrum Species
11.3.3 Reconstruction of Molecular Phylogeny of Clerodendrum Species Based on ITS2 Sequence
11.4 Discussion
References
12: Population Genetic Diversity of Dysoxylum Binectariferum, an Economically Important Tree Species of the Western Ghats, Ind...
12.1 Introduction
12.2 Materials and Methods
12.2.1 Study Species
12.2.1.1 Study Sites
12.2.1.2 DNA Extraction and PCR Amplification of SSR Primers
12.2.2 Estimating Genetic Variability
12.2.3 Population Differentiation and Gene Flow
12.3 Results
12.4 Population Differentiation and Gene Flow
12.5 Genetic Diversity in Adult and Seedlings of D. Binectariferum
12.6 Discussion
12.6.1 Overall Genetic Diversity in D. Binectariferum
12.6.2 Effect of Fragmentation and Genetic Diversity in Adult and Seedlings of D. Binectariferum
12.6.3 Genetic Differentiation of D. Binectariferum
12.6.4 Implications for Conservation
References
13: Gut Metagenomics of Pati Hanh (Anas platyrhynchos domesticus)
13.1 Introduction
13.2 Gut Health
13.2.1 Enzyme Benefit in Poultry Diet
13.2.2 Poultry Intestinal Microbiome Affects Host Immune Function
13.2.3 Poultry Intestinal Microbiome and Detoxification
13.2.4 The Role of the Microbiome in Reducing Pathogens
13.3 Microbes Screening through Metagenomics
13.3.1 Metagenomic DNA Extraction
13.3.1.1 Extraction of DNA by Direct Method
13.3.1.2 Extraction of DNA by the Indirect Method
13.3.2 Screening of Metagenomes
13.3.2.1 Function-Based Screening
13.3.2.2 Sequence-Based Screening
13.3.3 Bioinformatics Tools for Functional Metagenomic Data Annotation
13.4 Conclusion and Future Perspective
References
14: Morphological and Molecular Characterization of Genome Types in Wild and Cultivated Bananas (Musa Species) of Two States i...
14.1 Introduction
14.2 Materials and Methods
14.2.1 Field Survey and Sample Collection
14.2.2 Characterization of Genome Groups of Musa Specimens
14.2.2.1 Morphological Score Card Method
14.2.2.2 Inter-Retrotransposon Amplified Polymorphism (IRAP) Based Molecular Method
IRAP-PCR
14.3 Results
14.3.1 Genome Types of Musa Specimens from North Eastern India Based on Modified Genome Score Card System
14.4 Genome Characterization of Musa Specimens Using IRAP Marker
14.4.1 IRAP Polymorphism among Musa Specimens
14.5 Discussion
14.5.1 Genome Types of Wild and Cultivated Musa Specimens from North Eastern India Based on the Morphological Genome Scoring S...
14.5.2 Genome Types of Wild and Cultivated Musa Specimens from North Eastern India Based on IRAP Profiles
References
15: Pollen Digital Image Mapping and Its Symmetrical Correlation Using MATLAB
15.1 Introduction
15.2 Method of Slide Preparation
15.3 Results and Discussion
15.3.1 Palynological Mapping of Pollens from Haryana, India
15.4 Applications
15.4.1 Environment
15.4.2 Pollination for Reproduction
15.4.3 Palynology and Forensic Science
15.5 Conclusions
References
16: Role of Next-Generation Sequencing (NGS) in Understanding the Microbial Diversity
16.1 Introduction to Microbial World
16.2 The Invisible World of Microbes and its Global Impact
16.3 Metagenomics: A Way Forward in Microbial Ecology
16.4 Ways to Study Metagenomes
16.5 Next-Generation Sequencing Platforms to Explore Metagenomes
16.6 Roche 454 Genome Sequencer
16.7 Illumina Genome Sequencer
16.8 Qiagen Gene Reader
16.9 ABI SOLiD (Sequencing by Oligonucleotide Ligation and Detection) System
16.10 Ion Torrent Sequencing Technology (PGM, Proton, S5 Series)
16.11 The Third Generation of Sequencing
16.12 Technological Leap and the Changing Landscape of Biological Research
16.13 Applications for Microbiology
16.14 Basic Steps in Metagenomic Data Analysis
16.15 Future Perspective of Metagenomics
16.16 Conclusions
References