Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

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Abstract

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

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The online version of this article (doi:10.1186/s12864-017-3862-8) contains supplementary material, which is available to authorized users.

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Most cited references 44

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The zebrafish reference genome sequence and its relationship to the human genome.

Kerstin Howe, Matthew D. Clark, Carlos F Torroja … (2013)

Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

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The genomic basis of adaptive evolution in threespine sticklebacks

Felicity Jones, Manfred Grabherr, Yingguang Frank Chan … (2012)

Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature.

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Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters

Alika Maunakea, Raman P. Nagarajan, Mikhail Bilenky … (2010)

While the methylation of DNA in 5′ promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear 1–5 . In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5′ CpG island (CGI) promoters, while a far greater proportion occurs across gene bodies, coinciding with highly conserved sequences 5–10 . Tissue-specific intragenic methylation might reduce, 3 or, paradoxically, enhance transcription elongation efficiency 1,2,4,5 . Capped analysis of gene expression (CAGE) experiments also indicate that transcription commonly initiates within and between genes 11–15 . To investigate the role of intragenic methylation, we generated a map of DNA methylation from human brain encompassing 24.7 million of the 28 million CpG sites. From the dense, high-resolution coverage of CpG islands, the majority of methylated CpG islands were revealed to be in intragenic and intergenic regions, while less than 3% of CpG islands in 5′ promoters were methylated. The CpG islands in all three locations overlapped with RNA markers of transcription initiation, and unmethylated CpG islands also overlapped significantly with trimethylation of H3K4, a histone modification enriched at promoters 16 . The general and CpG-island-specific patterns of methylation are conserved in mouse tissues. An in-depth investigation of the human SHANK3 locus 17,18 and its mouse homologue demonstrated that this tissue-specific DNA methylation regulates intragenic promoter activity in vitro and in vivo. These methylation-regulated, alternative transcripts are expressed in a tissue and cell type-specific manner, and are expressed differentially within a single cell type from distinct brain regions. These results support a major role for intragenic methylation in regulating cell context-specific alternative promoters in gene bodies.

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Author and article information

Contributors

Daniel J. Macqueen: daniel.macqueen@abdn.ac.uk

Craig R. Primmer:

ORCID: http://orcid.org/0000-0002-3687-8435

craig.primmer@helsinki.fi

Ross D. Houston: ross.houston@roslin.ed.ac.uk

Barbara F. Nowak: b.nowak@utas.edu.au

Ben F. Koop: bkoop@uvic.ca

Sigbjørn Lien: sigbjorn.lien@nmbu.no

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 27 June 2017

Publication date PMC-release: 27 June 2017

Publication date Collection: 2017

Volume: 18

Electronic Location Identifier: 484

Affiliations

[1 ]ISNI 0000 0004 1936 7291, GRID grid.7107.1, Institute of Biological and Environmental Sciences, , University of Aberdeen, ; Aberdeen, AB24 2TZ UK

[2 ]ISNI 0000 0001 2097 1371, GRID grid.1374.1, Department of Biology, , University of Turku, ; 20014 Turku, Finland

[3 ]ISNI 0000 0004 1936 7988, GRID grid.4305.2, The Roslin Institute and Royal (Dick) School of Veterinary Studies, , The University of Edinburgh, ; Midlothian, EH25 9RG UK

[4 ]ISNI 0000 0004 1936 826X, GRID grid.1009.8, Institute for Marine and Antarctic Studies, , University of Tasmania, ; Launceston, TAS Australia

[5 ]ISNI 0000 0004 1936 8390, GRID grid.23856.3a, Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), , Université Laval, ; Québec, G1V 0A6 Canada

[6 ]ISNI 0000000109409492, GRID grid.13985.36, , The Research Council of Norway, ; Drammensveien 288, P.O. Box 564, NO-1327 Lysaker, Norway

[7 ]ISNI 0000 0004 1936 7494, GRID grid.61971.38, Department of Molecular Biology and Biochemistry, , Simon Fraser University, ; Burnaby, BC V5A 1S6 Canada

[8 ]ISNI 0000 0001 2298 9663, GRID grid.5380.e, Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, , Universidad de Concepción, ; 4030000 Concepción, Chile

[9 ]ISNI 0000 0000 9049 5051, GRID grid.418188.c, , Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, ; Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany

[10 ]GRID grid.460202.2, , INRA, UR1037 Fish Physiology and Genomics, ; Rennes, France

[11 ]ISNI 0000 0004 0385 4466, GRID grid.443909.3, Human Genetics Program ICBM Faculty of Medicine, , University of Chile, ; Santiago, Chile

[12 ]CSIRO Agriculture, QLD, St Lucia, 4067 Australia

[13 ]ISNI 0000 0004 1936 9465, GRID grid.143640.4, Department of Biology, , University of Victoria, ; Victoria, BC V8W 3N5 Canada

[14 ]ISNI 0000 0004 0607 975X, GRID grid.19477.3c, Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, , Norwegian University of Life Sciences, ; NO-1432 Ås, Norway

[15 ]ISNI 0000 0004 0385 4466, GRID grid.443909.3, Center for Mathematical Modelling, Department of Mathematical Engineering, , University of Chile, ; 8370456 Santiago, Chile

[16 ]ISNI 0000 0004 0385 4466, GRID grid.443909.3, Center for Genome Regulation, , University of Chile, ; 8370456 Santiago, Chile

[17 ]ISNI 0000000123318773, GRID grid.7872.a, School of Biological, Earth and Environmental Sciences, , University College Cork, ; Cork, Ireland

[18 ]ISNI 0000 0001 2156 804X, GRID grid.412848.3, Center for Biomedical Research, , Universidad Andres Bello, ; 8370146 Santiago, Chile

[19 ]ISNI 0000 0001 2156 804X, GRID grid.412848.3, FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, , Universidad Andres Bello, ; 8370146 Santiago, Chile

[20 ]ISNI 0000000122986657, GRID grid.34477.33, School of Aquatic and Fishery Sciences, , University of Washington, ; Box 355020, Seattle, WA 98195 USA

[21 ]ISNI 0000 0001 1502 9269, GRID grid.420104.3, , Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, ; 2725 Montlake Blvd E, Seattle, WA 98112 USA

[22 ]ISNI 0000 0004 0442 8784, GRID grid.425499.7, , Matis Ltd, ; Vínlandsleið 12, 113 Reykjavík, Iceland

[23 ]ISNI 0000 0001 1516 2393, GRID grid.5947.f, , NTNU - Norwegian University of Science and Technology, ; NO-7491 Trondheim, Norway

[24 ]ISNI 0000 0004 0404 0958, GRID grid.463419.d, National Center for Cool and Cold Water Aquaculture, , USDA ARS, ; 11861 Leetown Road, Kearneysville, WV 25430 USA

[25 ]GRID grid.17089.37, Department of Agricultural, Food, and Nutritional Science, , University of Alberta, ; Edmonton, AB Canada

[26 ]ISNI 0000 0004 0404 0958, GRID grid.463419.d, Office of National Programs, , USDA ARS, ; 5601 Sunnyside Avenue, Beltsville, MD 20705-5148 USA

[27 ]ISNI 0000 0000 9130 6822, GRID grid.25055.37, Department of Ocean Sciences, , Memorial University of Newfoundland, ; 1 Marine Lab Road, St. John’s, NL A1C 5S7 Canada

[28 ]ISNI 0000 0000 9336 0638, GRID grid.453288.0, , Genome British Columbia, ; Suite 400 – 575, West 8th Avenue, Vancouver, BC V5Z 0C4 Canada

[29 ]ISNI 0000 0001 2288 9830, GRID grid.17091.3e, Department of Zoology, , University of British Columbia, ; 6270 University Blvd, Vancouver, BC V6T 1Z4 Canada

[30 ]Instituto Tecnológico del Salmón S.A., INTESAL de SalmonChile, Puerto Montt, Chile

[31 ]ISNI 0000 0001 2191 5013, GRID grid.412179.8, Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, , University of Santiago, ; 9170022 Santiago, Chile

[32 ]ISNI 0000 0004 0427 3161, GRID grid.10917.3e, , Institute of Marine Research, ; P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway

[33 ]ISNI 0000 0004 0385 4466, GRID grid.443909.3, Faculty of Veterinary and Animal Sciences, , University of Chile, ; Av. Santa Rosa 11735, Santiago, Chile & Aquainnovo, Cardonal s/n, Puerto Montt, Chile

Author information

Craig R. Primmer http://orcid.org/0000-0002-3687-8435

Article

Publisher ID: 3862

DOI: 10.1186/s12864-017-3862-8

PMC ID: 5488370

PubMed ID: 28655320

SO-VID: b258e3bb-88a6-4643-92de-06559e03acf7

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 11 October 2016

Date accepted : 14 June 2017

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000199, U.S. Department of Agriculture;

Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;

Award ID: BB/P02582X/1

Award Recipient : Samuel A. M. Martin

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: salmonid fish,genome biology,functional annotation,comparative biology,standardized data and metadata,data sharing,aquaculture,whole genome duplication,evolution,phenotyping

Data availability:

ScienceOpen disciplines: Genetics

Keywords: salmonid fish, genome biology, functional annotation, comparative biology, standardized data and metadata, data sharing, aquaculture, whole genome duplication, evolution, phenotyping

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

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Genome Integrity

Most cited references 44

The zebrafish reference genome sequence and its relationship to the human genome.

The genomic basis of adaptive evolution in threespine sticklebacks

Conserved Role of Intragenic DNA Methylation in Regulating Alternative Promoters

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