The Atlantic salmon genome provides insights into rediploidization View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-05

AUTHORS

Sigbjørn Lien, Ben F. Koop, Simen R. Sandve, Jason R. Miller, Matthew P. Kent, Torfinn Nome, Torgeir R. Hvidsten, Jong S. Leong, David R. Minkley, Aleksey Zimin, Fabian Grammes, Harald Grove, Arne Gjuvsland, Brian Walenz, Russell A. Hermansen, Kris von Schalburg, Eric B. Rondeau, Alex Di Genova, Jeevan K. A. Samy, Jon Olav Vik, Magnus D. Vigeland, Lis Caler, Unni Grimholt, Sissel Jentoft, Dag Inge Våge, Pieter de Jong, Thomas Moen, Matthew Baranski, Yniv Palti, Douglas R. Smith, James A. Yorke, Alexander J. Nederbragt, Ave Tooming-Klunderud, Kjetill S. Jakobsen, Xuanting Jiang, Dingding Fan, Yan Hu, David A. Liberles, Rodrigo Vidal, Patricia Iturra, Steven J. M. Jones, Inge Jonassen, Alejandro Maass, Stig W. Omholt, William S. Davidson

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. More... »

PAGES

200

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature17164

    DOI

    http://dx.doi.org/10.1038/nature17164

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1005725135

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27088604


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