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The Atlantic salmon genome provides insights into rediploidization
Lien, S.; Koop, B.F.; Sandve, S.R.; Miller, J.R.; Kent, M.P.; Nome, T.; Hvidsten, T.R.; Leong, J.S.; Minkley, D.R.; Zimin, A.; Grammes, F.; Grove, H.; Gjuvsland, A.; Walenz, B.; Hermansen, R.A.; von Schalburg, K.; Rondeau, E.B.; Di Genova, A.; Samy, J.K.A.; Olav Vik, J.; Vigeland, M.D.; Caler, L.; Grimholt, U.; Jentoft, S.; Våge, D.I.; de Jong, P.J.; Moen, T.; Baranski, M.; Palti, Y. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature (Lond.) 533(7602): 200-205. http://dx.doi.org/10.1038/nature17164
In: Nature: International Weekly Journal of Science. Nature Publishing Group: London. ISSN 0028-0836; e-ISSN 1476-4687, more
Peer reviewed article  

Available in  Authors 

Keywords
    Biological phenomena > Evolution
    Genomes
    Salmo salar Linnaeus, 1758 [WoRMS]
    Marine/Coastal

Authors  Top 
  • Lien, S.
  • Koop, B.F.
  • Sandve, S.R.
  • Miller, J.R.
  • Kent, M.P.
  • Nome, T.
  • Hvidsten, T.R.
  • Leong, J.S.
  • Minkley, D.R.
  • Zimin, A.
  • Grammes, F.
  • Grove, H.
  • Gjuvsland, A.
  • Walenz, B.
  • Hermansen, R.A.
  • von Schalburg, K.
  • Rondeau, E.B.
  • Di Genova, A.
  • Samy, J.K.A.
  • Olav Vik, J.
  • Vigeland, M.D.
  • Caler, L.
  • Grimholt, U.
  • Jentoft, S.
  • Våge, D.I., more
  • de Jong, P.J.
  • Moen, T.
  • Baranski, M.
  • Palti, Y.

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.

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