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Authors: Lien, Sigbjørn and Koop, Ben F and Sandve, Simen R and Miller, Jason R and Kent, Matthew P and Nome, Torfinn and Hvidsten, Torgeir R and Leong, Jong S and Minkley, David R and Zimin, Aleksey and Grammes, Fabian and Grove, Harald and Gjuvsland, Arne and Walenz, Brian and Hermansen, Russell A and von Schalburg, Kris and Rondeau, Eric B and Di Genova, Alex and Samy, Jeevan K A and Olav Vik, Jon and Vigeland, Magnus D and Caler, Lis and Grimholt, Unni and Jentoft, Sissel and Inge Våge, Dag and de Jong, Pieter and Moen, Thomas and Baranski, Matthew and Palti, Yniv and Smith, Douglas R and Yorke, James A and Nederbragt, Alexander J and Tooming-Klunderud, Ave and Jakobsen, Kjetill S and Jiang, Xuanting and Fan, Dingding and Hu, Yan and Liberles, David A and Vidal, Rodrigo and Iturra, Patricia and Jones, Steven J M and Jonassen, Inge and Maass, Alejandro and Omholt, Stig W and Davidson, William S

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.

Journal: Nature
DOI: 10.1038/nature17164
Year: 2016

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