Sampling of Riverine or Marine Bacterial Communities in Remote Locations: From Field to Publication -- DNA Extraction Protocols for Whole Genome Sequencing in Marine Organisms -- High-Throughput Sequencing of Complete Mitochondrial Genomes -- Phylogenomics Using Transcriptome Data -- SNP Discovery Using Next Generation Transcriptomic Sequencing -- SNP-Arrays for Species Identification in Salmonids -- The Next Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR -- Using Environmental DNA for Invasive Species Surveillance and Monitoring -- Microarrays/DNA Chips for the Detection of Waterborne Pathogens -- DNA Barcoding of Marine Metazoans -- DNA Barcoding Marine Biodiversity: Steps from Mere Cataloguing to Giving Reasons for Biological Differences -- Metabarcoding Marine Sediments: Preparation of Amplicon Libraries -- Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Dual-PCR Method -- Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Adaptor-Ligation Method -- Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME -- Analysis of Illumina MiSeq Metabarcoding Data: Application to Benthic Indices for Environmental Monitoring.

This volume presents the latest protocols for both laboratory and bioinformatics based analyses in the field of marine genomics. The chapters presented in the book cover a wide range of topics, including the sampling and genomics of bacterial communities, DNA extraction in marine organisms, high-throughput sequencing of whole mitochondrial genomes, phylogenomics, SNP discovery, SNP-arrays for species identification, digital PCR-based quantification methods, environment DNA for invasive species surveillance and monitoring, microarrays for the detection of waterborne pathogens, DNA barcoding of marine biodiversity, metabarcoding protocols for marine eukaryotes, analytical protocols for the visualization of eukaryotic diversity, and applications for genomic data to benthic indices for environmental monitoring. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Marine Genomics: Methods and Protocols is a valuable resource for researchers, students, and policy makers in the field of marine biology. .