Journal
NATURE
Volume 533, Issue 7602, Pages 200-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nature17164
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Funding
- Research Council of Norway (NFR)
- Norwegian Seafood Research Fund
- Genome BC
- Chilean Economic Development Agency - CORFO and InnovaChile Committee
- Marine Harvest
- AquaGen
- Cermaq
- Salmobreed
- NFR [208481/F50, 226266, 225181, 221734/030]
- Natural Sciences and Engineering Research Council (NSERC), Canada
- University of Victoria
- ARS [ARS-0427931, 813654] Funding Source: Federal RePORTER
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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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