The Atlantic salmon genome provides insights into rediploidization

Sigbjørn Lien, Ben F. Koop, Simen R. Sandve, Jason R. Miller, Matthew P. Kent, Torfinn Nome, Torgeir R. Hvidsten, Jong S. Leong, David R. Minkley, Aleksey Zimin, Fabian Grammes, Harald Grove, Arne Gjuvsland, Brian Walenz, Russell A. Hermansen, Kris von Schalburg, Eric B. Rondeau, Alex Di Genova, Jeevan K. A. Samy, Jon Olav Vik, Magnus D. Vigeland, Lis Caler, Unni Grimholt, Sissel Jentoft, Dag Inge Våge, Pieter de Jong, Thomas Moen, Matthew Baranski, Yniv Palti, Douglas R. Smith, James A. Yorke, Alexander J. Nederbragt, Ave Tooming-Klunderud, Kjetill S. Jakobsen, Xuanting Jiang, Dingding Fan, Yan Hu, David A. Liberles, Rodrigo Vidal, Patricia Iturra, Steven J. M. Jones, Inge Jonassen, Alejandro Maass, Stig W. Omholt () and William S. Davidson ()
Additional contact information
Sigbjørn Lien: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Ben F. Koop: University of Victoria, Victoria
Simen R. Sandve: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Jason R. Miller: J. Craig Venter Institute
Matthew P. Kent: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Torfinn Nome: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Torgeir R. Hvidsten: Biotechnology and Food Science, Norwegian University of Life Sciences
Jong S. Leong: University of Victoria, Victoria
David R. Minkley: University of Victoria, Victoria
Aleksey Zimin: Institute for Physical Sciences and Technology, University of Maryland
Fabian Grammes: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Harald Grove: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Arne Gjuvsland: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Brian Walenz: J. Craig Venter Institute
Russell A. Hermansen: University of Wyoming
Kris von Schalburg: University of Victoria, Victoria
Eric B. Rondeau: University of Victoria, Victoria
Alex Di Genova: Center for Mathematical Modeling, University of Chile
Jeevan K. A. Samy: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Jon Olav Vik: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Magnus D. Vigeland: Medical Genetics, Oslo University Hospital and University of Oslo
Lis Caler: J. Craig Venter Institute
Unni Grimholt: Norwegian Veterinary Institute
Sissel Jentoft: Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo
Dag Inge Våge: Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences
Pieter de Jong: CHORI
Thomas Moen: AquaGen
Matthew Baranski: Nofima
Yniv Palti: National Center for Cool and Cold Water Aquaculture, ARS-USDA
Douglas R. Smith: Beckman Genomics, Danvers
James A. Yorke: University of Wyoming
Alexander J. Nederbragt: Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo
Ave Tooming-Klunderud: Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo
Kjetill S. Jakobsen: Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo
Xuanting Jiang: BGI-Shenzhen
Dingding Fan: BGI-Shenzhen
Yan Hu: BGI-Shenzhen
David A. Liberles: Center for Computational Genetics and Genomics, Temple University
Rodrigo Vidal: Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, University of Santiago
Patricia Iturra: Faculty of Medicine, University of Chile
Steven J. M. Jones: Genome Sciences Centre, BC Cancer Agency, Vancouver
Inge Jonassen: University of Bergen
Alejandro Maass: Center for Mathematical Modeling, University of Chile
Stig W. Omholt: Centre for Biodiversity Dynamics, NTNU - Norwegian University of Science and Technology
William S. Davidson: Simon Fraser University

Nature, 2016, vol. 533, issue 7602, 200-205

Abstract: 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.

Date: 2016
References: Add references at CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
https://www.nature.com/articles/nature17164 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:533:y:2016:i:7602:d:10.1038_nature17164

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/nature17164

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().