The Atlantic salmon genome provides insights into rediploidization
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2016Metadata
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Lien, Sigbjorn
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The Atlantic salmon genome provides insights into rediploidization
Author
- Lien, Sigbjorn;
- Koop, Ben F.;
- Sandve, Simen R.;
- Miller, Jason R.;
- Kent, Matthew P.;
- Nome, Torfinn;
- Hvidsten, Torgeir R.;
- Leong, Jong S.;
- Minkley, David R.;
- Zimin, Aleksey;
- Grammes, Fabián;
- Grove, Harald;
- Gjuvsland, Arne;
- Walenz, Brian;
- Hermansen, Russell A.;
- von Schalburg, Kris;
- Rondeau, Eric B.;
- Di Genova, Alex;
- Samy, Jeevan;
- Vik, Jon Olav;
- Vigeland, Magnus D.;
- Caler, Lis;
- Grimholt, Unni;
- Jentoft, Sissel;
- Vage, Dag Inge;
- de Jong, Pieter;
- Moen, Thomas;
- Baranski, Matthew;
- Palti, Yniv;
- Smith, Douglas R.;
- Yorke, James A.;
- Nederbragt, Alexander J.;
- Tooming-Klunderud, Ave;
- Jakobsen, Kjetill S.;
- Jiang, Xuanting;
- Fan, Dingding;
- Liberles, David A.;
- Vidal, Rodrigo;
- Iturra Constant, Patricia;
- Jones, Steven J.;
- Jonassen, Inge;
- Maass Sepúlveda, Alejandro;
- Omholt, Stig W.;
- Davidson, William S.;
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.
Patrocinador
Research Council of Norway (NFR)
Norwegian Seafood Research Fund
Genome BC
Chilean Economic Development Agency - CORFO and InnovaChile Committee
Marine Harvest
AquaGen
Cermaq
Salmobreed
NFR
208481/F50
226266
225181
221734/030
Natural Sciences and Engineering Research Council (NSERC), Canada
University of Victoria
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Nature | Vol 533 | 12 May 2016
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