The Atlantic salmon genome provides insights into rediploidization

Article, Other ORP type English OPEN
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. ... view all 45 authors (2016)
  • Publisher: Nature Publishing Group
  • Journal: (issn: 0028-0836)
  • Related identifiers: doi: 10.1038/nature17164
  • Subject: Biological Sciences | Biologiska vetenskaper

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. This work is licensed under a Creative Commons Attribution 4.0 International License.
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