Marine Genomics: Methods and Protocols

265 Pages·2016·6.882 MB·English

by  Sarah J. Bourlat

Methods in
Molecular Biology 1452
Sarah J. Bourlat Editor
Marine
Genomics
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
For further volumes:
http://www.springer.com/series/7651

Marine Genomics
Methods and Protocols
Edited by
Sarah J. Bourlat
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Editor
Sarah J . B ourlat
Department of Marine Sciences
University of Gothenburg
Gothenburg, Sweden
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-3772-1 ISBN 978-1-4939-3774-5 (eBook)
DOI 10.1007/978-1-4939-3774-5
Library of Congress Control Number: 2016943834
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Cover caption: Ephyra larva of the barrel jellyfi sh, Rhizostoma pulmo captured in a zooplankton haul off the Swedish
west coast. – Photo By: Erik Selander, Department of Marine Sciences, University of Gothenburg, Sweden
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Prefa ce
Marine genomics includes all aspects of genes and genomes of marine organisms aimed at
understanding their evolution, function, biodiversity and environmental interactions. The
fi eld of genomics has been revolutionized by next generation sequencing, providing novel
insights into one of the largest biomes on our planet.
In this book, we present the latest protocols for both laboratory and bioinformatics
based analyses in the fi eld of marine genomics. The chapters presented here 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 identifi cation, digital
PCR-based quantifi cation methods, environmental 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 of genomic data to benthic
indices for environmental monitoring.
These trusted protocols provide detailed step-by-step instructions, regents and materi-
als as well as tips and troubleshooting, making this volume a valuable resource for research-
ers, students, and policy makers in the fi eld of marine biology.
Gothenburg, Sweden Sarah J . Bourlat
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Sampling of Riverine or Marine Bacterial Communities
in Remote Locations: From Field to Publication. . . . . . . . . . . . . . . . . . . . . . . 1
Katja Lehmann
2 DNA Extraction Protocols for Whole-Genome Sequencing
in Marine Organisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Marina P anova , H enrik Aronsson , R. Andrew C ameron , Peter Dahl ,
Anna G odhe , Ulrika Lind , O lga Ortega-Martinez , R icardo Pereyra ,
Sylvie V . M . Tesson , A nna-Lisa Wrange , A nders Blomberg ,
and K erstin J ohannesson
3 High-Throughput Sequencing of Complete Mitochondrial Genomes . . . . . . . 4 5
Andrew G eorge B riscoe , K evin Peter Hopkins , and Andrea Waeschenbach
4 Phylogenomics Using Transcriptome Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 5
Johanna T aylor Cannon and K evin Michael Kocot
5 SNP Discovery Using Next Generation Transcriptomic Sequencing. . . . . . . . . 8 1
Pierre D e W it
6 SNP Arrays for Species Identification in Salmonids . . . . . . . . . . . . . . . . . . . . . 9 7
Roman W enne , A gata D rywa , M atthew K ent , Kristil Kindem Sundsaasen ,
and Sigbjørn L ien
7 The Next-Generation PCR-Based Quantification Method
for Ambient Waters: Digital PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 13
Yiping C ao , John F. Griffith , and Stephen B. Weisberg
8 Using Environmental DNA for Invasive Species Surveillance
and Monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 31
Andrew R . M ahon and Christopher L. Jerde
9 Microarrays/DNA Chips for the Detection of Waterborne Pathogens. . . . . . . 1 43
Filipa F . V ale
10 DNA Barcoding of Marine Metazoans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 55
Dirk Steinke , S ean W. J . Prosser , and Paul D. N. Hebert
11 DNA Barcoding Marine Biodiversity: Steps from Mere Cataloguing
to Giving Reasons for Biological Differences. . . . . . . . . . . . . . . . . . . . . . . . . . 169
Mikko N ikinmaa and M iriam Götting
12 Metabarcoding Marine Sediments: Preparation of Amplicon Libraries. . . . . . . 1 83
Vera G . F onseca and Delphine L allias
13 P reparation of Amplicon Libraries for Metabarcoding of Marine
Eukaryotes Using Illumina MiSeq: The Dual-PCR Method. . . . . . . . . . . . . . . 197
Sarah J . Bourlat , Q uiterie Haenel , Jennie Finnman , and Matthieu L eray
vii
viii Contents
14 Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes
Using Illumina MiSeq: The Adapter Ligation Method. . . . . . . . . . . . . . . . . . . 209
Matthieu L eray , Q uiterie Haenel , and Sarah J. Bourlat
15 Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding
Data Using QIIME. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Matthieu L eray and Nancy K nowlton
16 Analysis of Illumina MiSeq Metabarcoding Data: Application
to Benthic Indices for Environmental Monitoring. . . . . . . . . . . . . . . . . . . . . . 237
Eva A ylagas and Naiara R odríguez-Ezpeleta
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 51
Contributors
HENRIK A RONSSON • Department of Biological and Environmental Sciences ,
University of Gothenburg , G othenburg, Sweden
EVA A YLAGAS • AZTI, Marine Research Division , S ukarrieta, Bizkaia, S pain
ANDERS B LOMBERG • Department of Marine Sciences, University of Gothenburg , S trömstad,
Sweden
SARAH J. B OURLAT • Department of Marine Sciences, University of Gothenburg ,
Gothenburg, S weden
ANDREW G EORGE BRISCOE • Department of Life Sciences, N atural History Museum ,
London, UK
R. A NDREW CAMERON • Division of Biology and Biological Engineering, California
Institute of Technology , Pasadena, CA , U SA
JOHANNA TAYLOR C ANNON • Department of Zoology, Naturhistoriska Riksmuseet ,
Stockholm, Sweden
YIPING CAO • Southern California Coastal Water Research Project Authority , Costa Mesa,
CA , U SA
PETER DAHL • Department of Chemistry and Molecular Biology, University of Gothenburg ,
Gothenburg, Sweden
AGATA DRYWA • Institute of Oceanology, P olish Academy of Sciences , S opot , Poland
JENNIE FINNMAN • Sahlgrenska Academy, G othenburg University Genomics Core Facility ,
Gothenburg, S weden
VERA G . F ONSECA • Zoological Research Museum Alexander Koenig (ZFMK), C entre for
Molecular Biodiversity Research , Bonn, Germany
ANNA G ODHE • Department of Marine Sciences, University of Gothenburg , G othenburg,
Sweden
MIRIAM GÖTTING • Department of Biology, U niversity of Turku , T urku , F inland
JOHN F . GRIFFITH • Southern California Coastal Water Research Project Authority ,
Costa Mesa, C A , USA
QUITERIE H AENEL • Department of Biology and Environmental Sciences, University of
Gothenburg , G othenburg, S weden
PAUL D . N. H EBERT • Centre for Biodiversity Genomics, Biodiversity Institute of Ontario,
University of Guelph , Guelph, ON, Canada
KEVIN P ETER H OPKINS • Department of Life Sciences, Natural History Museum , London, UK
CHRISTOPHER L. J ERDE • Department of Biology, Aquatic Ecosystems Analysis Laboratory ,
University of Nevada , R eno , N V , U SA
KERSTIN JOHANNESSON • Department of Marine Sciences, U niversity of Gothenburg ,
Strömstad, S weden
MATTHEW K ENT • Centre for Integrative Genetics (CIGENE), Department of Animal and
Aquacultural Sciences, IHA, Norwegian University of Life Sciences, NMBU , Å s , N orway
NANCY K NOWLTON • National Museum of Natural History , S mithsonian Institution ,
Washington, DC, U SA
ix