The Atlantic salmon genome provides insights into rediploidization

Published 2016

Publication details

Journal : Nature , vol. 533 , p. 200–205 , 2016

International Standard Numbers :
Printed : 0028-0836
Electronic : 1476-4687

Publication type : Academic article

Contributors : Baranski, Matthew; Davidson, William S; Gjuvsland, Arne Bjørke; Grammes, Fabian; Grimholt, Unni; Grove, Harald; Hvidsten, Torgeir Rhoden; Jakobsen, Kjetill Sigurd; Jentoft, Sissel; Jonassen, Inge; Kent, Matthew Peter; Lien, Sigbjørn; Miller, Jason R.; Moen, Thomas; Nederbragt, Alexander J.; Nome, Torfinn; Omholt, Stig William; Samy, Jeevan Karloss Antony; Sandve, Simen Rød; Tooming-Klunderud, Ave; Vigeland, Magnus Dehli; Vik, Jon Olav; Våge, Dag Inge; Walenz, Brian

Issue : 7602

Links :
DOI : doi.org/10.1038/nature17164
ARKIV : hdl.handle.net/11250/2480787

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Summary

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.