Keywords:
Genomics.
;
Marine biology.
;
Electronic books.
Description / Table of Contents:
Marine biology has always played an important role in biological research, being at the origin of many key advances. To a certain extent, the influence of marine biology on the biological sciences was overshadowed over a period of several years by the remarkable advances that were made using powerful model organisms from terrestrial environments. This situation is now changing again, however, due primarily to spectacular developments in genomic methodologies that have significantly accelerated research in a broad spectrum of marine biology disciplines ranging from biodiversity to developmental biology to biotechnology. The data generated by marine genomics projects have had an impact on questions as diverse as understanding planetary geochemical cycles, the impact of climate change on marine fauna and flora, the functioning of marine ecosystems, the discovery of new organisms and novel biomolecules, and investigation of the evolution of animal developmental complexity. This book represents the first attempt to document how genomic technologies are revolutionising these diverse domains of marine biology. Each chapter of this book looks at how these technologies are being employed in a specific domain of marine research and provides a summary of the major results obtained to date. The book as a whole provides an overview of marine genomics as a discipline and represents an ideal starting point for exploring this rapidly developing domain.
Type of Medium:
Online Resource
Pages:
1 online resource (410 pages)
Edition:
1st ed.
ISBN:
9789048186396
Series Statement:
Advances in Marine Genomics Series ; v.1
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=993291
DDC:
572.861177
Language:
English
Note:
Intro -- Preface -- Contents -- Contributors -- 1 Genomics in the Discovery and Monitoring of Marine Biodiversity -- 1.1 Marine Biodiversity and Genomics A Global Perspective -- 1.1.1 Marine Biodiversity: Structural and Functional Components -- 1.1.2 The Nature of Marine Biodiversity -- 1.1.3 Empirical and Conceptual Advances -- 1.2 Molecular Identification of Marine Biodiversity -- 1.2.1 Diversity and Functional Analyses of Microbial Communities -- 1.2.2 Between the Microbes and Metazoans: Eukaryotic Protists -- 1.2.2.1 Ribosomal Probes -- 1.2.2.2 Biodiversity Assessment at Sub-species Level -- 1.2.3 Diversity and Ecological Analyses of Benthic Meiofaunal Communities -- 1.2.4 DNA Barcoding and Fisheries -- 1.2.5 Larvae in Marine Systems -- 1.3 Marine Biodiversity and Ecosystem Function -- 1.3.1 Microbes in Novel Environments -- 1.3.2 Microbial Links in Ecosystem Processes -- 1.3.3 Environmental Change and Microbial Diversity -- 1.4 Concluding Remarks -- References -- 2 Metagenome Analysis -- 2.1 Introduction -- 2.2 History and Application of Metagenomics -- 2.3 Technical Challenges in Metagenome Analysis -- 2.3.1 Strategies to Assess the Metagenome -- 2.3.2 Enrichment Strategies -- 2.3.3 Isolation and Purification of Genomic DNA -- 2.3.4 Amplification of Genomic DNA -- 2.3.5 Construction and Analysis of Metagenomic Libraries -- 2.3.5.1 Small Insert Metagenomic Libraries -- 2.3.5.2 Large Insert Metagenomic Libraries -- 2.3.5.3 Metagenomic Library Size -- 2.3.5.4 Storage of Metagenomic Libraries -- 2.3.5.5 Screening of Metagenomic Libraries -- 2.3.6 Library Independent Metagenome Analysis -- 2.4 Bioinformatic Challenges in Metagenome Analysis -- 2.4.1 Fragment Assembly assembly and Binning -- 2.4.2 Gene Prediction -- 2.4.3 Functional Annotation -- 2.4.4 Web Based Annotation Pipelines -- 2.4.5 Annotation Systems for Local Installation.
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2.4.6 High Diversity Environments, Shallow Sequencing and Short Read Technologies -- 2.4.7 Metagenome Descriptors for Comparative Metagenomics -- 2.4.7.1 Phylogenetic Diversity -- 2.4.7.2 Functional Diversity -- 2.5 Outlook -- References -- 3 Populations and Pathways: Genomic Approachesto Understanding Population Structure and EnvironmentalAdaptation -- 3.1 Tools -- 3.1.1 DNA and RNA Studies: EST Libraries -- 3.1.2 DNA Studies: Microsatellites -- 3.1.3 DNA Studies: Single Nucleotide Polymorphisms (SNPs) -- 3.1.4 DNA Studies: Amplified Fragment Length Polymorphisms (AFLPs) -- 3.1.5 DNA Studies: High Through-Put Sequencing -- 3.1.6 DNA and RNA Studies: Targeted Gene Analyses -- 3.1.7 DNA Studies: Barcoding -- 3.1.8 RNA Studies: Microarrays or Gene Chips -- 3.1.9 RNA Studies: Q-PCR -- 3.2 Population Genomics -- 3.2.1 Analysis: Choices, Limitations and Considerations -- 3.2.1.1 Marker Type -- 3.2.1.2 Differentiating Selective and Demographic Effects -- 3.2.1.3 Identifying Adaptive Traits -- 3.3 Practical Application of Population Genomics in the Marine Environment -- 3.3.1 Dispersal in the Sea: From Larval Development to Local Adaptation and Speciation Processes -- 3.3.1.1 Pelagic Larval Studies -- 3.3.1.2 Genetic Basis of Adaptive Differentiation in High Gene Flow Species -- 3.3.1.3 Study of Hybrid Zones and the Speciation Processes -- 3.3.2 Marine Bio-Invasions: Using Genomic Resources to Study Invasive Species -- 3.3.3 Uncovering the Genetic Basis of Hybrid Vigour in Aquaculture Populations -- 3.3.4 Gene Polymorphism and Population Adaptation -- 3.4 Expression Studies and Environmental Genomics -- 3.4.1 Defining Habitat Limits: Biogeography -- 3.4.2 Microarrays: Identification of Biochemical Pathways Involved in Adaptation -- 3.4.3 Genome Plasticity and Seasonal Variation -- 3.4.4 Adaptation to Extreme Environments -- 3.4.4.1 Hydrothermal Vents.
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3.4.4.2 Polar Environments -- 3.4.4.3 Ecotoxicology Monitoring -- 3.5 Summary and Future Issues -- References -- 4 Phylogeny of Animals: Genomes Have a Lot to Say -- 4.1 Introduction -- 4.2 The Roots of Animal Phylogeny -- 4.2.1 Historical Schemes Are Based on the Coelom Evolution Hypotheses -- 4.2.2 Sorting More Characters Through a Cladistic Approach -- 4.2.3 Small Ribosomal RNA Gene and the ''New View'' of Animal Phylogeny -- 4.2.4 The Limits of the ''New View'' -- 4.3 The Power and Pitfalls of Phylogenomics -- 4.4 Phylogenomics Resolves Animal Relationships -- 4.4.1 Battle over the Coelomata and the Importance of Taxonomic Sampling -- 4.4.1.1 Early Phylogenomic Attempts Challenged the ''New View'' -- 4.4.1.2 Coelomata and the Interpretation of Rare Genomic Changes -- 4.4.2 Is It Actually Possible to Decipher Animal Relationships? -- 4.5 Toward a Broad Phylogenomic Picture of Metazoan Relationships -- 4.5.1 Challenging Well-Established Clades: The Case of Deuterostomes -- 4.5.2 Chaetognaths Fit into the Bilaterian Tree -- 4.5.3 Acoel Flatworms, Basal or Not? -- 4.5.4 Deeper into Protostome Relationships -- 4.6 Conclusion: The Future of Animal Phylogeny -- References -- 5 Metazoan Complexity -- 5.1 Approaches to Complexity -- 5.2 Choanoflagellates: The Evolution of Multicellularity in Metazoa -- 5.3 Sponges: The Evolution of Animal Development, Body Axis, Cell Types and Epithelia -- 5.4 The Placozoan Trichoplax: A Primitively Simple or Highly Reduced Metazoan? -- 5.5 Cnidaria: A Simple Body with a Complex Genome -- 5.5.1 The Nematostella Genome -- 5.5.2 Cnidarian BMP Patterning and the Evolution of the Bilaterian Dorso-Ventral Axis -- 5.5.3 Cnidarian Hox Genes and the Evolution of the Antero-Posterior Axis -- 5.5.4 The Homology of Body Axes Between Cnidaria and Bilateria -- 5.5.5 Cnidarians and the Evolution of Mesoderm.
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5.5.6 ''Cryptic'' Complexity in Cnidarians? -- 5.6 Ecdysozoans: Going Beyond the Established Systems -- 5.7 Lophotrochozoans: An Evolutionary Branch Leading to New Perspectives -- 5.8 Aplysia: From Neural Circuits to Neurotranscriptomics -- 5.9 Platynereis: Ancestral Complexity of Cells and Genomic Features -- 5.10 Alternative Splicing: Modulating the Basic Layers of Genomic Complexity? -- 5.11 Sea Urchins: Unexpected Functional Repertoires at the Base of Deuterostomes -- 5.12 Lancelets and the Chordate Prototype -- 5.13 Ascidians: Changes and Constants in Developmental Programmes -- 5.14 Perspectives -- References -- 6 Genomics of Marine Algae -- 6.1 What Are Algae? -- 6.2 Why Algae Are Interesting -- 6.3 Endosymbiosis and the Origins of the Algae -- 6.4 Algae and Marine Ecosystems -- 6.4.1 Diversification of the Phytoplankton During the Evolution of the Earth -- 6.4.2 Algae Are Important Components of the Phytoplankton -- 6.4.3 Exploration of Planktonic Ecosystems Using High-Throughput Sequencing -- 6.4.4 Diversity and Dynamics of Planktonic Ecosystems -- 6.4.5 Organism-Based Approaches for Exploring the Biology of Planktonic Algae -- 6.4.5.1 Diatom Genomics -- 6.4.5.2 Prasinophyte Genomics -- 6.4.5.3 Other Microalgal Genome Projects -- 6.4.5.4 Dinoflagellates -- 6.4.6 Macroalgal Genomics -- 6.4.6.1 Brown Macroalgae -- 6.4.6.2 Red Macroalgae -- 6.4.6.3 Green Macroalgae -- 6.5 Future Research in Algal Genomics -- References -- 7 Genomic Approaches in Aquaculture and Fisheries -- 7.1 Introduction -- 7.2 Genomic Tools and Resources -- 7.2.1 Genetic Linkage Maps -- 7.2.2 Radiation Hybrid (RH) Maps -- 7.2.3 BAC-Based Physical Maps -- 7.2.4 High Quality Draft Genome Sequences -- 7.2.5 Functional Genomic Tools -- 7.3 Genomic Approaches in Breeding and Reproduction -- 7.4 Genomic Approaches in Growth and Nutrition -- 7.4.1 Introduction.
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7.4.2 Transcriptomic Changes in Skeletal Muscle Related to Muscle Growth -- 7.4.3 Transcriptomic Changes in Skeletal Muscle Related to External Factors -- 7.4.4 Genomic Approaches to the Study of Hepatic Function -- 7.4.4.1 Transcriptional Changes in the Liver in Relation to Growth and Nutrition -- 7.4.4.2 Changes in the Liver Proteome in Relation to Nutrition and Growth -- 7.4.5 Conclusions and Future Directions -- 7.5 Genomic Approaches in Product Quality and Safety -- 7.5.1 Seafood Quality Has a Multifactorial Background -- 7.5.2 Fish Quality Traits Assessed by Genomic and Proteomic Methods -- 7.5.2.1 Colour -- 7.5.2.2 Texture (as Muscle Cellularity) -- 7.5.2.3 Texture (as Affected by Postmortem Degradation) -- 7.5.2.4 Nutritional Quality and Health Value -- 7.5.3 Other Emerging Quality Traits -- 7.5.4 Seafood Safety -- 7.5.4.1 Health Hazards in Seafood -- 7.5.4.2 Allergenicity in Seafood Products -- 7.5.5 Seafood Authentication and Traceability -- 7.6 Genomic Approaches in HostPathogen Interaction -- 7.6.1 Host--Parasite Interactions in Fish -- 7.6.2 Transcriptomic Characterization of Host Immune Response -- 7.6.2.1 EST Analysis to Identify Genes Involved in Host Immune Response -- 7.6.2.2 Microarray Analysis to Identify Genes Involved in Host Immune Response -- 7.6.2.3 Real-Time PCR to Identify Candidate Markers for Disease Detection -- 7.6.3 How Can Genetic Linkage, RH and Physical Maps Contribute to Shedding Light on Fish--Pathogen Interactions? -- 7.6.4 Host--Parasite Interactions in Shellfish -- 7.6.4.1 Improvement of Diagnostic Tools Using Molecular Approaches -- 7.6.4.2 Molecular Immunity of Bivalves -- 7.6.4.3 Immune Response to Perkinsus Infection -- 7.6.4.4 Immune Response to Vibrio Infection -- 7.6.4.5 Status of Transcriptomic Tools -- 7.6.4.6 Conclusions.
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7.7 Genomic Variation, Stock Structure, Adaptation and Traceability in Natural Fish Populations.
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