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Marine Genomics

Methods and Protocols

  • Book
  • © 2016

Overview

Editors:
  1. Sarah J. Bourlat

    1. Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden

    View editor publications

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1452)

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About this book

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.

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

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

    • Katja Lehmann
    Pages 1-11

  3. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms

    • Marina Panova, Henrik Aronsson, R. Andrew Cameron, Peter Dahl, Anna Godhe, Ulrika Lind et al.
    Pages 13-44

  4. High-Throughput Sequencing of Complete Mitochondrial Genomes

    • Andrew George Briscoe, Kevin Peter Hopkins, Andrea Waeschenbach
    Pages 45-64

  5. Phylogenomics Using Transcriptome Data

    • Johanna Taylor Cannon, Kevin Michael Kocot
    Pages 65-80

  6. SNP Discovery Using Next Generation Transcriptomic Sequencing

    • Pierre De Wit
    Pages 81-95

  7. SNP Arrays for Species Identification in Salmonids

    • Roman Wenne, Agata Drywa, Matthew Kent, Kristil Kindem Sundsaasen, Sigbjørn Lien
    Pages 97-111

  8. The Next-Generation PCR-Based Quantification Method for Ambient Waters: Digital PCR

    • Yi** Cao, John F. Griffith, Stephen B. Weisberg
    Pages 113-130

  9. Using Environmental DNA for Invasive Species Surveillance and Monitoring

    • Andrew R. Mahon, Christopher L. Jerde
    Pages 131-142

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

    • Filipa F. Vale
    Pages 143-153

  11. DNA Barcoding of Marine Metazoans

    • Dirk Steinke, Sean W. J. Prosser, Paul D. N. Hebert
    Pages 155-168

  12. DNA Barcoding Marine Biodiversity: Steps from Mere Cataloguing to Giving Reasons for Biological Differences

    • Mikko Nikinmaa, Miriam Götting
    Pages 169-182

  13. Metabarcoding Marine Sediments: Preparation of Amplicon Libraries

    • Vera G. Fonseca, Delphine Lallias
    Pages 183-196

  14. Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Dual-PCR Method

    • Sarah J. Bourlat, Quiterie Haenel, Jennie Finnman, Matthieu Leray
    Pages 197-207

  15. Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Adapter Ligation Method

    • Matthieu Leray, Quiterie Haenel, Sarah J. Bourlat
    Pages 209-218

  16. Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME

    • Matthieu Leray, Nancy Knowlton
    Pages 219-235

  17. Analysis of Illumina MiSeq Metabarcoding Data: Application to Benthic Indices for Environmental Monitoring

    • Eva Aylagas, Naiara Rodríguez-Ezpeleta
    Pages 237-249

  18. Back Matter

    Pages 251-253
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Editors and Affiliations

  • Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden

    Sarah J. Bourlat

Bibliographic Information

  • Book Title: Marine Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Sarah J. Bourlat

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-3774-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2016

  • Hardcover ISBN: 978-1-4939-3772-1Published: 27 July 2016

  • Softcover ISBN: 978-1-4939-8135-9Published: 31 May 2018

  • eBook ISBN: 978-1-4939-3774-5Published: 26 July 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 253

  • Number of Illustrations: 22 b/w illustrations, 24 illustrations in colour

  • Topics: Human Genetics

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