The Atlantic salmon genome provides insights into rediploidization

By S. Lien, B. Koop, S. Sandve, Jason Rafe Miller, M. Kent, T. Nome, T. R. Hvidsten, Jong S Leong, D. Minkley, Aleksey V. Zimin and 35 more. Nature, 2016

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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.

Subfields: Aquatic Science, Genetics, Immunology

View Paper: https://www.semanticscholar.org/paper/e44ccf7e6f7176934dcf8adfb9abc7b7062c7c37

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Citations in the corpus

Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants (2019, background): “In addition, Z. mays experienced an additional species-specific event (mWGD, ~ 26 Mya) [50].”
Deriving genotypes from RAD-seq short-read data using Stacks (2017, background): “For non-model organisms, often a reference genome for a specific species does not exist, but perhaps a phylogenetically closely related genome does (e.g., dozens of researchers work in various salmonid fishes, but the Atlantic salmon is the highest-quality reference genome available 40 ).”
Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions (2017, positive): “As a result of the above developments, and helped by the development of advanced genomic resources for the salmon (Houston et al., 2014; Lien et al., 2016; Tsai et al., 2016), QTL and genome-based selection is now being utilized in several of the commercial breeding programmes.”