Preface	6
	Contents	10
	Contributors	12
	1 Genomics in the Discovery and Monitoring of Marine Biodiversity	16
	1.1 Marine Biodiversity and Genomics A Global Perspective	16
	1.1.1 Marine Biodiversity: Structural and Functional Components	16
	1.1.2 The Nature of Marine Biodiversity	21
	1.1.3 Empirical and Conceptual Advances	21
	1.2 Molecular Identification of Marine Biodiversity	23
	1.2.1 Diversity and Functional Analyses of Microbial Communities	25
	1.2.2 Between the Microbes and Metazoans: Eukaryotic Protists	27
	1.2.2.1 Ribosomal Probes	27
	1.2.2.2 Biodiversity Assessment at Sub-species Level	28
	1.2.3 Diversity and Ecological Analyses of Benthic Meiofaunal Communities	29
	1.2.4 DNA Barcoding and Fisheries	30
	1.2.5 Larvae in Marine Systems	32
	1.3 Marine Biodiversity and Ecosystem Function	36
	1.3.1 Microbes in Novel Environments	36
	1.3.2 Microbial Links in Ecosystem Processes	36
	1.3.3 Environmental Change and Microbial Diversity	37
	1.4 Concluding Remarks	38
	References	40
	2 Metagenome Analysis	48
	2.1 Introduction	48
	2.2 History and Application of Metagenomics	50
	2.3 Technical Challenges in Metagenome Analysis	52
	2.3.1 Strategies to Assess the Metagenome	52
	2.3.2 Enrichment Strategies	54
	2.3.3 Isolation and Purification of Genomic DNA	56
	2.3.4 Amplification of Genomic DNA	57
	2.3.5 Construction and Analysis of Metagenomic Libraries	60
	2.3.5.1 Small Insert Metagenomic Libraries	60
	2.3.5.2 Large Insert Metagenomic Libraries	60
	2.3.5.3 Metagenomic Library Size	62
	2.3.5.4 Storage of Metagenomic Libraries	63
	2.3.5.5 Screening of Metagenomic Libraries	64
	2.3.6 Library Independent Metagenome Analysis	64
	2.4 Bioinformatic Challenges in Metagenome Analysis	66
	2.4.1 Fragment Assembly assembly and Binning	67
	2.4.2 Gene Prediction	69
	2.4.3 Functional Annotation	69
	2.4.4 Web Based Annotation Pipelines	70
	2.4.5 Annotation Systems for Local Installation	71
	2.4.6 High Diversity Environments, Shallow Sequencing and Short Read Technologies	72
	2.4.7 Metagenome Descriptors for Comparative Metagenomics	73
	2.4.7.1 Phylogenetic Diversity	73
	2.4.7.2 Functional Diversity	74
	2.5 Outlook	75
	References	77
	3 Populations and Pathways: Genomic Approachesto Understanding Population Structure and EnvironmentalAdaptation	87
	3.1 Tools	88
	3.1.1 DNA and RNA Studies: EST Libraries	89
	3.1.2 DNA Studies: Microsatellites	90
	3.1.3 DNA Studies: Single Nucleotide Polymorphisms (SNPs)	91
	3.1.4 DNA Studies: Amplified Fragment Length Polymorphisms (AFLPs)	92
	3.1.5 DNA Studies: High Through-Put Sequencing	94
	3.1.6 DNA and RNA Studies: Targeted Gene Analyses	95
	3.1.7 DNA Studies: Barcoding	96
	3.1.8 RNA Studies: Microarrays or Gene Chips	96
	3.1.9 RNA Studies: Q-PCR	97
	3.2 Population Genomics	97
	3.2.1 Analysis: Choices, Limitations and Considerations	98
	3.2.1.1 Marker Type	98
	3.2.1.2 Differentiating Selective and Demographic Effects	100
	3.2.1.3 Identifying Adaptive Traits	100
	3.3 Practical Application of Population Genomics in the Marine Environment	104
	3.3.1 Dispersal in the Sea: From Larval Development to Local Adaptation and Speciation Processes	104
	3.3.1.1 Pelagic Larval Studies	104
	3.3.1.2 Genetic Basis of Adaptive Differentiation in High Gene Flow Species	105
	3.3.1.3 Study of Hybrid Zones and the Speciation Processes	106
	3.3.2 Marine Bio-Invasions: Using Genomic Resources to Study Invasive Species	107
	3.3.3 Uncovering the Genetic Basis of Hybrid Vigour in Aquaculture Populations	107
	3.3.4 Gene Polymorphism and Population Adaptation	109
	3.4 Expression Studies and Environmental Genomics	110
	3.4.1 Defining Habitat Limits: Biogeography	111
	3.4.2 Microarrays: Identification of Biochemical Pathways Involved in Adaptation	113
	3.4.3 Genome Plasticity and Seasonal Variation	113
	3.4.4 Adaptation to Extreme Environments	114
	3.4.4.1 Hydrothermal Vents	115
	3.4.4.2 Polar Environments	116
	3.4.4.3 Ecotoxicology Monitoring	118
	3.5 Summary and Future Issues	119
	References	120
	4 Phylogeny of Animals: Genomes Have a Lot to Say	133
	4.1 Introduction	133
	4.2 The Roots of Animal Phylogeny	135
	4.2.1 Historical Schemes Are Based on the Coelom Evolution Hypotheses	135
	4.2.2 Sorting More Characters Through a Cladistic Approach	136
	4.2.3 Small Ribosomal RNA Gene and the ''New View'' of Animal Phylogeny	139
	4.2.4 The Limits of the ''New View''	140
	4.3 The Power and Pitfalls of Phylogenomics	141
	4.4 Phylogenomics Resolves Animal Relationships	142
	4.4.1 Battle over the Coelomata and the Importance of Taxonomic Sampling	143
	4.4.1.1 Early Phylogenomic Attempts Challenged the ''New View''	143
	4.4.1.2 Coelomata and the Interpretation of Rare Genomic Changes	143
	4.4.2 Is It Actually Possible to Decipher Animal Relationships?	145
	4.5 Toward a Broad Phylogenomic Picture of Metazoan Relationships	146
	4.5.1 Challenging Well-Established Clades: The Case of Deuterostomes	146
	4.5.2 Chaetognaths Fit into the Bilaterian Tree	148
	4.5.3 Acoel Flatworms, Basal or Not?	148
	4.5.4 Deeper into Protostome Relationships	149
	4.6 Conclusion: The Future of Animal Phylogeny	149
	References	151
	5 Metazoan Complexity	156
	5.1 Approaches to Complexity	156
	5.2 Choanoflagellates: The Evolution of Multicellularity in Metazoa	159
	5.3 Sponges: The Evolution of Animal Development, Body Axis, Cell Types and Epithelia	163
	5.4 The Placozoan Trichoplax: A Primitively Simple or Highly Reduced Metazoan?	165
	5.5 Cnidaria: A Simple Body with a Complex Genome	167
	5.5.1 The Nematostella Genome	168
	5.5.2 Cnidarian BMP Patterning and the Evolution of the Bilaterian Dorso-Ventral Axis	169
	5.5.3 Cnidarian Hox Genes and the Evolution of the Antero-Posterior Axis	169
	5.5.4 The Homology of Body Axes Between Cnidaria and Bilateria	170
	5.5.5 Cnidarians and the Evolution of Mesoderm	172
	5.5.6 ''Cryptic'' Complexity in Cnidarians?	173
	5.6 Ecdysozoans: Going Beyond the Established Systems	174
	5.7 Lophotrochozoans: An Evolutionary Branch Leading to New Perspectives	175
	5.8 Aplysia: From Neural Circuits to Neurotranscriptomics	175
	5.9 Platynereis: Ancestral Complexity of Cells and Genomic Features	176
	5.10 Alternative Splicing: Modulating the Basic Layers of Genomic Complexity?	178
	5.11 Sea Urchins: Unexpected Functional Repertoires at the Base of Deuterostomes	179
	5.12 Lancelets and the Chordate Prototype	180
	5.13 Ascidians: Changes and Constants in Developmental Programmes	181
	5.14 Perspectives	182
	References	184
	6 Genomics of Marine Algae	192
	6.1 What Are Algae?	192
	6.2 Why Algae Are Interesting	193
	6.3 Endosymbiosis and the Origins of the Algae	194
	6.4 Algae and Marine Ecosystems	196
	6.4.1 Diversification of the Phytoplankton During the Evolution of the Earth	200
	6.4.2 Algae Are Important Components of the Phytoplankton	200
	6.4.3 Exploration of Planktonic Ecosystems Using High-Throughput Sequencing	201
	6.4.4 Diversity and Dynamics of Planktonic Ecosystems	203
	6.4.5 Organism-Based Approaches for Exploring the Biology of Planktonic Algae	204
	6.4.5.1 Diatom Genomics	205
	6.4.5.2 Prasinophyte Genomics	208
	6.4.5.3 Other Microalgal Genome Projects	210
	6.4.5.4 Dinoflagellates	211
	6.4.6 Macroalgal Genomics	212
	6.4.6.1 Brown Macroalgae	212
	6.4.6.2 Red Macroalgae	214
	6.4.6.3 Green Macroalgae	216
	6.5 Future Research in Algal Genomics	216
	References	217
	7 Genomic Approaches in Aquaculture and Fisheries	225
	7.1 Introduction	225
	7.2 Genomic Tools and Resources	227
	7.2.1 Genetic Linkage Maps	227
	7.2.2 Radiation Hybrid (RH) Maps	230
	7.2.3 BAC-Based Physical Maps	231
	7.2.4 High Quality Draft Genome Sequences	232
	7.2.5 Functional Genomic Tools	232
	7.3 Genomic Approaches in Breeding and Reproduction	234
	7.4 Genomic Approaches in Growth and Nutrition	237
	7.4.1 Introduction	238
	7.4.2 Transcriptomic Changes in Skeletal Muscle Related to Muscle Growth	238
	7.4.3 Transcriptomic Changes in Skeletal Muscle Related to External Factors	239
	7.4.4 Genomic Approaches to the Study of Hepatic Function	240
	7.4.4.1 Transcriptional Changes in the Liver in Relation to Growth and Nutrition	241
	7.4.4.2 Changes in the Liver Proteome in Relation to Nutrition and Growth	242
	7.4.5 Conclusions and Future Directions	243
	7.5 Genomic Approaches in Product Quality and Safety	243
	7.5.1 Seafood Quality Has a Multifactorial Background	244
	7.5.2 Fish Quality Traits Assessed by Genomic and Proteomic Methods	244
	7.5.2.1 Colour	245
	7.5.2.2 Texture (as Muscle Cellularity)	245
	7.5.2.3 Texture (as Affected by Postmortem Degradation)	246
	7.5.2.4 Nutritional Quality and Health Value	247
	7.5.3 Other Emerging Quality Traits	248
	7.5.4 Seafood Safety	249
	7.5.4.1 Health Hazards in Seafood	250
	7.5.4.2 Allergenicity in Seafood Products	250
	7.5.5 Seafood Authentication and Traceability	251
	7.6 Genomic Approaches in HostPathogen Interaction	252
	7.6.1 Host--Parasite Interactions in Fish	252
	7.6.2 Transcriptomic Characterization of Host Immune Response	253
	7.6.2.1 EST Analysis to Identify Genes Involved in Host Immune Response	253
	7.6.2.2 Microarray Analysis to Identify Genes Involved in Host Immune Response	253
	7.6.2.3 Real-Time PCR to Identify Candidate Markers for Disease Detection	254
	7.6.3 How Can Genetic Linkage, RH and Physical Maps Contribute to Shedding Light on Fish--Pathogen Interactions?	254
	7.6.4 Host--Parasite Interactions in Shellfish	255
	7.6.4.1 Improvement of Diagnostic Tools Using Molecular Approaches	255
	7.6.4.2 Molecular Immunity of Bivalves	256
	7.6.4.3 Immune Response to Perkinsus Infection	257
	7.6.4.4 Immune Response to Vibrio Infection	259
	7.6.4.5 Status of Transcriptomic Tools	260
	7.6.4.6 Conclusions	261
	7.7 Genomic Variation, Stock Structure, Adaptation and Traceability in Natural Fish Populations	261
	7.7.1 The Major Issues	261
	7.7.2 State-of the Art in the Population Genomics of Fishes	264
	7.7.2.1 Identifying Population Structure and Dynamics	264
	7.7.2.2 Selection and Adaptation in Natural and Exploited Populations	267
	7.7.2.3 Tracing Natural Populations for Fisheries Enforcement and Traceability	270
	7.7.2.4 Integrating Evolutionary and Ecological Functional Genomics with the Environment	272
	7.7.3 A Vision of the Future	274
	References	276
	8 Marine Biotechnology	299
	8.1 A Brief Description of the Field of Marine Biotechnology	299
	8.2 How Genomics Impacts on the Various Fields of Marine Biotechnology	301
	8.3 Expanding Gene Resources Through Microbial-Community Genomic Projects, Complete Genomes of Isolated Organisms and Data Mining	302
	8.3.1 Complete Genomes	303
	8.3.2 The Growing Contribution of Metagenomes	305
	8.4 Contribution of Marine Biotechnology to the Discovery of Natural Products, Novel Pharmaceuticals and White Technology	311
	8.4.1 Viruses	311
	8.4.2 Archaea and Bacteria	313
	8.4.3 Algae	313
	8.4.4 Algae for Biodiesel Production	314
	8.4.5 Algae for Ethanol Production	315
	8.4.6 Algae for Hydrogen Gas Production	315
	8.4.7 Algae for Biomass Fermentation	315
	8.4.8 Marine Genomics and Algal Biofuels	316
	8.4.9 Algae as a Cell Factory	316
	8.4.10 Marine Fungi	318
	8.4.11 Metazoans	318
	8.4.12 In Closing	319
	References	319
	9 Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions	326
	9.1 Sequence Data Generation	327
	9.1.1 Classical Genome Sequencing Approaches	327
	9.1.1.1 The Sanger Method	327
	9.1.1.2 Shotgun Technique	328
	9.1.1.3 Bacterial Genome Assembly and Finishing	328
	9.1.2 Next Generation of Genome Sequencing	329
	9.1.2.1 Pyrosequencing or 454 Sequencing	331
	9.1.2.2 Illumina 0 Sequencing Technology	331
	9.1.2.3 SOLiD 0 System	332
	9.1.3 Other New Advanced Approaches to DNA Sequencing	332
	9.1.3.1 Open-Source ''Polony Sequencing'' System	332
	9.1.3.2 Sequencing-by-Hybridization	333
	9.1.3.3 Nanopore Sequencing	333
	9.1.4 Conclusion	333
	9.2 Data Management for Bioinformatics Applications	334
	9.2.1 Data Modelling and Storage	334
	9.2.2 Data Access	335
	9.2.3 Common File Formats	337
	9.3 DNA Sequence Analysis	337
	9.3.1 EST Processing	337
	9.3.2 Gene Prediction	342
	9.3.2.1 Gene Finding in Prokaryotes	342
	9.3.2.2 Gene Finding in Eukaryotes	344
	9.3.3 Genome Annotation and Beyond	348
	9.3.3.1 Introduction to Sequence Similarity	348
	9.3.3.2 From Gene Annotation to Genome Annotation	349
	9.3.3.3 Protein Annotation Tools	350
	9.3.4 Comparative Genomics and Functional Classification	353
	9.3.4.1 Homology and Similarity	353
	9.3.4.2 Protein Domains	355
	9.3.4.3 Use of Gene Clusters in Functional Annotation	355
	9.3.4.4 Existing Resources for Comparative Analyses	356
	9.3.5 Major Public Sequences Databases and Other Resources	358
	9.3.5.1 Major Public Nucleotide Sequences Databases	358
	9.3.5.2 Major Public Protein Sequences Database: UniProt	362
	9.3.5.3 RefSeq	364
	9.3.5.4 Other Resources	365
	9.4 Transcriptome Analysis Using High-Throughput Technology	367
	9.4.1 Fundamentals of Microarray Technology	370
	9.4.1.1 Variation and Replication	371
	9.4.1.2 How Many Replicates?	372
	9.4.2 Gene Expression Analysis	372
	9.4.2.1 Image Analysis	372
	9.4.2.2 Normalization	373
	9.4.2.3 Detecting Significant Changes	374
	9.4.2.4 Cluster Analysis	376
	9.4.2.5 Classification	376
	9.4.2.6 Microarray Software	377
	9.4.2.7 Image Analysis Software	377
	9.4.2.8 Pure Analysis Systems	378
	9.4.2.9 General Purpose Database Systems	378
	9.4.2.10 R and BioConductor	378
	9.4.3 Data Sharing and Public Repositories	379
	9.4.4 Summary of the Gene Expression Analysis Section	380
	References	381
	Glossary	390
	Index	400