The Atlantic salmon genome provides insights into rediploidization
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| Authors: | Lien, S; Koop, BF; Sandve, SR; Miller, JR; Kent, MP; Nome, T; Hvidsten, TR; Leong, JS; Minkley, DR; Zimin, A; Grammes, F; Grove, H; Gjuvsland, A; Walenz, B; Hermansen, RA; von Schalburg, K; Rondeau, EB; Di Genova, A; Samy, JKA; Vik, JO; Vigeland, MD; Caler, L; Grimholt, U; Jentoft, S; Vage, DI; de Jong, P; Moen, T; Baranski, M; Palti, Y; Smith, DR; Yorke, JA; Nederbragt, AJ; Tooming-Klunderud, A; Jakobsen, KS; Jiang, XT; Fan, DD; Liberles, DA; Vidal, R; Iturra, P; Jones, SJM; Jonassen, I; Maass, A; Omholt, SW; Davidson, WS |
| Year: | 2016 |
| Journal: | Nature 533: 200-+ Article Link (DOI) |
| Title: | The Atlantic salmon genome provides insights into rediploidization |
| 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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