Genomics in Aquaculture

291 Pages·2016·8.23 MB·English

by  Simon A MacKenzie

Genomics in Aquaculture
Edited by
Simon MacKenzie
Institute of Aquaculture
University of Stirling
Stirling, United Kingdom
Sissel Jentoft
Department of Biosciences
Centre for Ecological and Evolutionary
Synthesis (CEES)
University of Oslo, Oslo, Norway
Department of Natural Sciences
University of Agder, Kristiansand, Norway
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List of Contributors
José Antonio Álvarez-Dios Department of Genetics, Faculty of Biology (CIBUS),
University of Santiago de Compostela; Department of Applied Mathematics, Faculty
of Mathematics, University of Santiago de Compostela, Santiago de Compostela, Spain
Peter Aleström Department of Basic Sciences and Aquatic Medicine, Norwegian
University of Life Sciences, Oslo, Norway
Michaël Bekaert The Genetics and Reproduction Research Group, Institute of
Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
Camille Berthelot European Molecular Biology Laboratory, European Bioinfor-
matics Institute, Welcome Trust Genome Campus, Cambridge, United Kingdom;
CEA-Genomic Institute, French National Sequencing Center, Evry Cedex, France
Julien Bobe INRA, Fish Physiology and Genomics, Rennes, France
Pierre Boudinot Molecular Virology and Immunology, INRA, Université Paris-
Saclay, Jouy-en-Josas, France
Carmen Bouza Department of Genetics, Faculty of Veterinary, University of
Santiago de Compostela, Lugo, Spain
Manuel Gonzalo Claros Department of Molecular Biology and Biochemistry,
Faculty of Sciences, Campus de Teatinos s/n, University of Málaga; Plataforma
Andaluza de Bioinformática, University of Málaga, Málaga, Spain
Xavier Cousin IFREMER, Laboratory of Adaptation and Adaptabilities of Animal
and Systems (L3AS), Palavas and INRA, Laboratory of Fish Physiology and Genomics
(LPGP), Rennes, France
Hugues Roest Crollius Ecole Normale Supérieure (ENS), ENS Biology Institute,
IBENS, Paris, France
Jesús Fernández Departament of Animal Breeding, National Institute for Agricultural
and Food Research and Technology, Madrid, Spain
Antonio Figueras Marine Research Institute (IIM), Immunology & Genomics
group, Spanish National Research Council (CSIC), Vigo, Spain
x List of Contributors
Antonio Gómez-Tato Department of Genetics, Faculty of Biology (CIBUS), University
of Santiago de Compostela; Department of Geometry and Topology, Faculty of
Mathematics, University of Santiago de Compostela, Santiago de Compostela, Spain
Carine Genêt Animal Genetics and Integrative Biology, INRA, AgroParisTech,
Université Paris-Saclay, Jouy-en-Josas, France
Yann Guiguen INRA, Fish Physiology and Genomics, Rennes, France
Miguel Hermida Department of Genetics, Faculty of Veterinary, University of
Santiago de Compostela, Lugo, Spain
Olivier Jaillon CEA-Genomic Institute, French National Sequencing Center, Evry
Cedex, France
Kjetill S. Jakobsen Department of Biosciences, Centre for Ecological and Evolu-
tionary Synthesis (CEES), University of Oslo, Oslo, Norway
Sissel Jentoft Department of Biosciences, Centre for Ecological and Evolution-
ary Synthesis (CEES), University of Oslo, Oslo; Department of Natural Sciences,
University of Agder, Kristiansand, Norway
Yanliang Jiang Beijing Key Laboratory of Fishery Biotechnology, Centre for Ap-
plied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
Xingkun Jin Department of Biosciences, Centre for Ecological and Evolutionary
Synthesis (CEES), University of Oslo, Oslo, Norway
Yulin Jin The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Ge-
nomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of
Cell and Molecular Biosciences, Auburn University, Auburn, AL, United States
Jiongtang Li Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied
Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
Shikai Liu The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic
Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program
of Cell and Molecular Biosciences, Auburn University, Auburn, AL, United States
Zhanjiang Liu The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic
Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program
of Cell and Molecular Biosciences, Auburn University, Auburn, AL, United States
Simon MacKenzie Institute of Aquaculture, University of Stirling, Stirling, United
Kingdom
List of Contributors xi
Manuel Manchado IFAPA Center El Toruño, IFAPA, Consejeria de Agricultura y
Pesca, El Puerto de Santa María (Cádiz), Spain
Lucie Marandel Nutrition, metabolism and aquaculture (NUMEA), INRA, Univ
Pau & Pays Adour, Saint Pée sur Nivelle, France
Paulino Martínez Department of Genetics, Faculty of Veterinary, University of
Santiago de Compostela, Lugo, Spain
Brendan J. McAndrew The Genetics and Reproduction Research Group, Institute
of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
Rebeca Moreira Sanmartín Marine Research Institute (IIM), Immunology &
Genomics group, Spanish National Research Council (CSIC), Vigo, Spain
Alexander J. Nederbragt Department of Biosciences, Centre for Ecological and
Evolutionary Synthesis (CEES), University of Oslo; Department of Informatics,
Biomedical Informatics Research Group, University of Oslo, Oslo, Norway
Beatriz Novoa Institute of Marine Research (IIM), Spanish National Research
Council (CSIC), Vigo, Spain
Stéphane Panserat Nutrition, metabolism and aquaculture (NUMEA), INRA, Univ
Pau & Pays Adour, Saint Pée sur Nivelle, France
Belén G. Pardo Department of Genetics, Faculty of Veterinary, University of
Santiago de Compostela, Lugo, Spain
David J. Penman The Genetics and Reproduction Research Group, Institute of
Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
Patricia Pereiro Institute of Marine Research (IIM), Spanish National Research
Council (CSIC), Vigo, Spain
Francesc Piferrer Institute of Marine Sciences, Spanish National Research Council
(CSIC), Barcelona, Spain
Josep V. Planas Department of Physiology and Immunology, School of Biology,
University of Barcelona and Institute of Biomedicine (IBUB), Barcelona, Spain
Edwige Quillet Animal Genetics and Integrative Biology, INRA, AgroParisTech,
Université Paris-Saclay, Jouy-en-Josas, France
Laureana Rebordinos Laboratory of Genetics, Faculty of Environmental and Sea
Sciences, University of Cadiz, Polígono del Río San Pedro, Puerto Real, Cádiz, Spain
xii List of Contributors
Laia Ribas Institute of Marine Sciences, Spanish National Research Council
(CSIC), Barcelona, Spain
Matthew L. Rise Department of Ocean Sciences, Memorial University of
Newfoundland, St. John’s, NL, Canada
Steven Roberts School of Aquatic and Fishery Sciences University of Washington,
Seattle, WA, United Sates
Diego Robledo Department of Genetics, Faculty of Biology (CIBUS), University of
Santiago de Compostela, Santiago de Compostela, Spain
Silvia T. Rodríguez-Ramilo Departament of Animal Breeding, National Institute
for Agricultural and Food Research and Technology, Madrid, Spain; GenPhySE,
National Institute for Agricultural Research, Castanet-Tolosan, France
Juan A. Rubiolo Department of Genetics, Faculty of Veterinary, University of
Santiago de Compostela, Lugo, Spain
Bastiaan Star Department of Biosciences, Centre for Ecological and Evolutionary
Synthesis (CEES), University of Oslo, Oslo, Norway
Xiaowen Sun Heilongjiang Fishery Research Institute, Chinese Academy of Fisher-
ies Sciences, Harbin, China
Xoana Taboada Department of Genetics, Faculty of Biology (CIBUS), University
of Santiago de Compostela, Santiago de Compostela, Spain
Suxu Tan The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic
Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program
of Cell and Molecular Biosciences, Auburn University, Auburn, AL, United States
Ole Kristian Tørresen Department of Biosciences, Centre for Ecological and Evo-
lutionary Synthesis (CEES), University of Oslo, Oslo, Norway
Ana Viñas *Department of Genetics, Faculty of Veterinary, University of Santiago
de Compostela, Lugo, Spain
Jean-Nicolas Volff Institute of Functional Genomics of Lyon (IGFL), Ecole Normale
Supérieure de Lyon, CNRS, University of Lyon I, Lyon, France
Stefanie Wehner The Genetics and Reproduction Research Group, Institute of
Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
Hanne C. Winther-Larsen Department of Pharmaceutical Biosciences, School of
Pharmacy, University of Oslo, Oslo, Norway
List of Contributors xiii
Jian Xu Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied
Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
Peng Xu Beijing Key Laboratory of Fishery Biotechnology, Centre for Applied
Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing; State Key Labo-
ratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen
University, Xiamen, China
Yujia Yang The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic
Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program
of Cell and Molecular Biosciences, Auburn University, Auburn, AL, United States
Zihao Yuan The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic
Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, and Program
of Cell and Molecular Biosciences, Auburn University, Auburn, AL, United States
The new era of genome 1
sequencing using high-
throughput sequencing
technology: generation of the first
version of the Atlantic cod genome
Ole Kristian Tørresen*, Bastiaan Star*, Sissel Jentoft*,**, Kjetill S. Jakobsen*,
Alexander J. Nederbragt*,†
*Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES),
University of Oslo, Oslo, Norway; **Department of Natural Sciences, University of Agder,
Kristiansand, Norway; †Department of Informatics, Biomedical Informatics Research
Group, University of Oslo, Oslo, Norway
Introduction
The first vertebrate genomes to be completed—for example, the human genome
(Lander et al., 2001; Venter et al., 2001) and the genome of the teleost, fugu (Takifugu
rupriens) (Aparicio et al., 2002)—were sequenced using the only available technol-
ogy at that time, known as Sanger sequencing. This sequencing technology is expen-
sive in terms of cost per base, and due to the size of vertebrate genomes such projects
are labor intensive, necessitating large teams, and substantial funding. Still, most of
the model organisms were first sequenced using this method. In 2005, the first high-
throughput sequencing (HTS) technology, that is, massively parallel pyrosequencing
by Roche/454 (Margulies et al., 2005), was introduced, followed by Solexa/Illumina
(Bentley et al., 2008) in 2006. These technologies generate millions to billions of
bases in a single run, and therefore reduce labor intensity and cost per base by several
orders of magnitude. However, the read lengths produced by these technologies when
they first became available (25–35 bp for Illumina/Solexa (Illumina hereafter) and
100 bp for Roche/454 (454) were significantly shorter than for Sanger sequencing
(600–1000 bp). Due to fast technological improvements, the read lengths from the
HTS instruments soon became substantially longer, enabling sequencing and de novo
assembly (see Glossary) of large genomes using these technologies. As an effect, more
groups embarked on these kinds of projects. In 2008, however, such applications had
not yet been demonstrated on any vertebrate species, and de novo assembly programs
capable of handling the vast amounts of required short read data were not yet avail-
able. As a group working on evolutionary and ecological questions in fish, we saw the
ongoing technological developments as an opportunity to sequence and assemble a te-
leost genome using a pure HTS approach, at low cost and with a small research team.
Genomics in Aquaculture. http://dx.doi.org/10.1016/B978-0-12-801418-9.00001-9
Copyright © 2016 Elsevier Inc. All rights reserved.
2 Genomics in Aquaculture
In 2008, we were funded by the Research Council of Norway (RCN) to sequence
the genome of Atlantic cod (Gadus morhua L.) with the 454 sequencing technology.
Atlantic cod was chosen because of its impact as an economically important fishery
species, its considerable ecological and evolutionary scientific interest and its poten-
tial use in aquaculture. Furthermore, Atlantic cod has a relatively moderate genome
size (estimated to 830 million base pairs, Mbp)—making it a good target for the first
teleost genome sequenced with a pure HTS approach. In this chapter, we will describe
the sequencing, assembly, and annotation (see Glossary) of the Atlantic cod genome,
the specific findings related to the genome and future perspectives.
The first version of the Atlantic cod genome
The sequencing of a wild-caught cod specimen
The Atlantic cod-sequencing project was carried out with DNA isolated from a single
specimen. The specimen was wild-caught, male, approximately 8 years old, and origi-
nated from the North East Arctic cod (NEAC) population. This population is the most
abundant in the world (Ottersen et al., 2014; Kjesbu et al., 2014) and is of most signifi-
cance for Norwegian fisheries, with a value of the catch close to 4 billion Norwegian
Kroner (NOK) per year. The population exhibits seasonal migration from the Barents
Sea to its spawning ground along the Norwegian coast, the main one being the Lofoten
area, where there has been a traditional seasonal fishery for centuries.
DNA in eukaryotic cells is packaged in chromosomes, containing continuous, lin-
ear stretches often of millions of base pairs. In Atlantic cod, there are altogether 23
chromosomes comprising approximately 830 Mbp (Star et al., 2011). HTS technolo-
gies available at the time the project started are most efficient in sequencing short
stretches of DNA, usually substantially shorter than 1000 bp. An important step in
genome sequencing therefore consists of the physical fragmentation of these long
chromosomes, resulting in a set of small, randomly broken fragments of DNA. Us-
ing standard molecular biology approaches, these small fragments are then placed
between specific DNA molecules (adapters), which are recognized by the sequencing
machines. This process is called library preparation, and forms the start of any se-
quencing project. The sequencing of a single fragment from these libraries results in a
DNA sequence, which is called a read (Fig. 1.1). Overall, the procedure of physically
breaking the chromosomes and sequencing the resulting pieces is called “shotgun”
sequencing, a term which reflects the random fragmentation of the DNA sequences.
At the start of the sequencing project in 2009, two HTS technologies were avail-
able; Roche/454 and Illumina. Because of the longer read length of the 454 technol-
ogy and a wider range of suitable software utilizing those data at that time, we chose
to use this technology for the first version of the Atlantic cod genome. Unraveling the
genome of a species for the first time requires a large amount of data and often a range
of different sequencing libraries. During the first 10 months of 2009, we generated
the required amount of data using libraries made with DNA from the single Atlantic
cod (NEAC) specimen. A designated team of scientists kept the sequencing machines
The new era of genome sequencing using high-throughput sequencing technology 3
Figure 1.1 The creation of contigs and linking of contigs into scaffolds. (A) The assembler
finds reads with similar sequence and creates a contiguous consensus sequence from them,
which is called a contig. (B) The mapping of paired read information from libraries of
different insert size allows contigs to be ordered and oriented into scaffolds, with gaps
between the contigs represented by the gray dotted lines.
running as efficiently as possible. The final dataset consisted of approximately 64 mil-
lion reads and 33 billion base pairs (Gbp). Considering that the Atlantic cod genome
is 830 Mbp in size, the size of this dataset means that every nucleotide in the genome
is sequenced—on average—about 40 times, providing what is called 40× coverage
(also called oversampling). Most of the data were generated using the two 454 ma-
chines at the Norwegian Sequencing Centre, hosted by the Centre for Ecological and
Evolutionary Synthesis (CEES) at the University of Oslo.
The challenges of assembling large, outbred genomes
An important consequence of the random fragmentation of DNA for library prepa-
ration is that this process erases all long-range information of where the particular
fragments originally belong. Therefore, complex mathematical algorithms have been
designed to computationally combine these fragments in a single, coherent structure,
which is called an assembly. An assembly can be defined as “a hierarchical data struc-
ture that maps the sequence data to a putative reconstruction of the target [genome]”
(Miller et al., 2010).