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
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| 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.
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- 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.
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- Vigeland, M.D.
- Caler, L.
- Grimholt, U.
- Jentoft, S.
- Våge, D.I., more
- de Jong, P.J.
- Moen, T.
- Baranski, M.
- Palti, Y.
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| 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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