title: The Atlantic salmon genome provides insights into rediploidization.
abstract: The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: Ben F
authors.initials: BF
authors.lastname: Koop
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Simen R
authors.initials: SR
authors.lastname: Sandve
authors.affiliation: J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Miller
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Kent
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Torfinn
authors.initials: T
authors.lastname: Nome
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås NO-1432 Norway.|Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå 90187, Sweden.
authors.forename: Torgeir R
authors.initials: TR
authors.lastname: Hvidsten
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: Jong S
authors.initials: JS
authors.lastname: Leong
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: David R
authors.initials: DR
authors.lastname: Minkley
authors.affiliation: Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742-2431, USA.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Zimin
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Fabian
authors.initials: F
authors.lastname: Grammes
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Harald
authors.initials: H
authors.lastname: Grove
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Arne
authors.initials: A
authors.lastname: Gjuvsland
authors.affiliation: J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Walenz
authors.affiliation: Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA.|Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania 19122-6078, USA.|Department of Biology, Temple University, Philadelphia, Pennsylvania 19122-6078, USA.
authors.forename: Russell A
authors.initials: RA
authors.lastname: Hermansen
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: Kris
authors.initials: K
authors.lastname: von Schalburg
authors.affiliation: Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada.
authors.forename: Eric B
authors.initials: EB
authors.lastname: Rondeau
authors.affiliation: Center for Mathematical Modeling, University of Chile, Santiago 8370456, Chile.|Center for Genome Regulation, University of Chile, Santiago 8370415, Chile.
authors.forename: Alex
authors.initials: A
authors.lastname: Di Genova
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Jeevan K A
authors.initials: JK
authors.lastname: Samy
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Jon
authors.initials: J
authors.lastname: Olav Vik
authors.affiliation: Medical Genetics, Oslo University Hospital and University of Oslo, Oslo NO-0424, Norway.
authors.forename: Magnus D
authors.initials: MD
authors.lastname: Vigeland
authors.affiliation: J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA.
authors.forename: Lis
authors.initials: L
authors.lastname: Caler
authors.affiliation: Department of Virology, Norwegian Veterinary Institute, Oslo NO-0454, Norway.
authors.forename: Unni
authors.initials: U
authors.lastname: Grimholt
authors.affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway.
authors.forename: Sissel
authors.initials: S
authors.lastname: Jentoft
authors.affiliation: Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås NO-1432, Norway.
authors.forename: Dag Inge
authors.initials: DI
authors.lastname: Våge
authors.affiliation: CHORI, Oakland, California 94609, USA.
authors.forename: Pieter
authors.initials: P
authors.lastname: de Jong
authors.affiliation: AquaGen, Trondheim NO-7462, Norway.
authors.forename: Thomas
authors.initials: T
authors.lastname: Moen
authors.affiliation: Nofima, Tromsø NO-9291, Norway.
authors.forename: Matthew
authors.initials: M
authors.lastname: Baranski
authors.affiliation: National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, West Virginia 25430, USA.
authors.forename: Yniv
authors.initials: Y
authors.lastname: Palti
authors.affiliation: Beckman Genomics, Danvers, Massachusetts 01923, USA.|Courtagen Life Sciences, Woburn, Massachusetts 01801, USA.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Smith
authors.affiliation: Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Yorke
authors.affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Nederbragt
authors.affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway.
authors.forename: Ave
authors.initials: A
authors.lastname: Tooming-Klunderud
authors.affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway.
authors.forename: Kjetill S
authors.initials: KS
authors.lastname: Jakobsen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xuanting
authors.initials: X
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Dingding
authors.initials: D
authors.lastname: Fan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania 19122-6078, USA.|Department of Biology, Temple University, Philadelphia, Pennsylvania 19122-6078, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Liberles
authors.affiliation: Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Santiago 9170022, Chile.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Vidal
authors.affiliation: Faculty of Medicine, University of Chile, Santiago 8380453, Chile.
authors.forename: Patricia
authors.initials: P
authors.lastname: Iturra
authors.affiliation: Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada.|Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.affiliation: Department of Informatics, University of Bergen, Bergen NO-6020, Norway.
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
authors.affiliation: Center for Mathematical Modeling, University of Chile, Santiago 8370456, Chile.|Center for Genome Regulation, University of Chile, Santiago 8370415, Chile.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Maass
authors.affiliation: Centre for Biodiversity Dynamics, Department of Biology, NTNU - Norwegian University of Science and Technology, Trondheim NO-7491, Norway.
authors.forename: Stig W
authors.initials: SW
authors.lastname: Omholt
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
authors.forename: William S
authors.initials: WS
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mesh_terms: D000818:Animals; D004251:DNA Transposable Elements / Q000235:genetics; D004171:Diploidy; D019143:Evolution, Molecular; D005260:Female; D020440:Gene Duplication / Q000235:genetics*; D020131:Genes, Duplicate / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D023281:Genomics; D008297:Male; D008957:Models, Genetic; D016296:Mutagenesis / Q000235:genetics; D010802:Phylogeny; D012015:Reference Standards; D020317:Salmo salar / Q000145:classification / Q000235:genetics*; D017385:Sequence Homology
chemical_list: D004251:DNA Transposable Elements