The Atlantic salmon genome provides insights into rediploidization

• Published in: Nature
• Main Authors: Lien, Sigbjørn, Koop, Ben F, Sandve, Simen Rød, Miller, Jason R., Kent, Matthew Peter, Nome, Torfinn, Hvidsten, Torgeir Rhoden, Leong, Jong, Minkley, David R., Zimin, Aleksey, Grammes, Fabian, Grove, Harald, Gjuvsland, Arne Bjørke, Walenz, Brian, Hermansen, Russell A., von Schalburg, Kristian R., Rondeau, Eric, Genova, Alex Di, Antony Samy, Jeevan Karloss, Vik, Jon Olav, Vigeland, Magnus Dehli, Caler, Lis, Grimholt, Unni, Jentoft, Sissel, Våge, Dag Inge, de Jong, Pieter J., Moen, Thomas, Baranski, Matthew, Palti, Yniv, Smith, Douglas W., Yorke, James A., Nederbragt, Alexander J., Tooming-Klunderud, Ave, Jakobsen, Kjetill Sigurd, Jiang, Xuanting, Fan, Dingding, Hu, Yan, Liberles, David A., Vidal, Rodrigo, Iturra, Patricia, Jones, Steven J.M., Jonassen, Inge, Maass, Alejandro, Omholt, Stig William, Davidson, William S
• Format: Article in Journal/Newspaper
• Language: English
• Published: Macmillan Publishers Ltd. 2016
• Subjects: Atlantic salmon; Salmo salar
• Online Access: http://hdl.handle.net/10852/63167; http://urn.nb.no/URN:NBN:no-65729; https://doi.org/10.1038/nature17164

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.