Main description:

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.

Contents:

1.
Sampling
of Riverine or Marine Bacterial Communities in Remote Locations: From Field to Publication
Katja
Lehmann

2. DNA Extraction Protocols for Whole Genome Sequencing
in Marine Organisms
Marina Panova, Henrik Aronsson, R. Andrew
Cameron, Peter Dahl, Anna Godhe, Ulrika Lind, Olga Ortega-Martinez, Ricardo
Pereyra, Sylvie V. M. Tesson, Anna-Lisa Wrange, Anders Blomberg, Kerstin
Johannesson

3. High-Throughput
Sequencing of Complete Mitochondrial Genomes
Andrew George Briscoe,
Kevin Peter Hopkins, and Andrea Waeschenbach

4. Phylogenomics
Using Transcriptome Data
Johanna Taylor Cannon and Kevin Michael Kocot

5.
SNP
Discovery Using Next Generation Transcriptomic Sequencing
Pierre de Wit

6.
SNP-Arrays for Species Identification in
Salmonids
Roman Wenne, Agata Drywa, Matthew Kent,
Kristil Kindem Sundsaasen, Sigbjorn Lien

7.
The
Next Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR
Yiping Cao, John F. Griffith, and
Stephen B. Weisberg

8.
Using Environmental DNA for Invasive Species
Surveillance and Monitoring
Andrew R. Mahon and Christopher L. Jerde

9.
Microarrays/DNA Chips for the Detection
of Waterborne Pathogens

10.
DNA Barcoding of Marine Metazoans
Dirk Steinke, Sean W.J. Prosser, and
Paul D.N. Hebert

11.
DNA Barcoding Marine Biodiversity: Steps
from Mere Cataloguing to Giving Reasons for Biological Differences
Mikko Nikinmaa
and Miriam Goetting

12. Metabarcoding Marine Sediments: Preparation of Amplicon LibrariesVera G. Fonseca and
Delphine Lallias

13.
Preparation of Amplicon Libraries for Metabarcoding
of Marine Eukaryotes Using Illumina MiSeq: The Dual-PCR Method
Sarah J. Bourlat, Quiterie Haenel, Jennie
Finnman, and Matthieu Leray

14.
Preparation of Amplicon Libraries for Metabarcoding
of Marine Eukaryotes Using Illumina MiSeq: The Adaptor-Ligation Method
Matthieu Leray,
Quiterie Haenel, and Sarah J. Bourlat

15.
Visualizing Patterns of Marine Eukaryotic
Diversity from Metabarcoding Data Using QIIME
Matthieu Leray and Nancy Knowlton

16. Analysis
of Illumina MiSeq Metabarcoding Data: Application to Benthic Indices for Environmental
Monitoring
Eva Aylagas and Naiara Rodriguez-Ezpeleta