Marine Genomics: Methods and Protocols

ISBN-13: 9781493937721 / Angielski / Twarda / 2016 / 253 str.

Sarah J. Bourlat

Opis

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.

Spis treści

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, Sigbjørn 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
<Filipa Vale

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 Götting

12. Metabarcoding Marine Sediments: Preparation of Amplicon Libraries

Vera 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 Rodríguez-Ezpeleta