Introduction to Marine Genomics

Cover13; -- 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 -- 1.2.3 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 -- 2.3.6 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 -- 2.4.6 High Diversity Environments, Shallow Sequencing and Short Read Technologies -- 2.4.7 Metagenome Descriptors for Comparative Metagenomics -- 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 -- 3.3 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 -- 3.3.2 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 -- 3.5 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.