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author Lien, Sigbjørn
Koop, Ben F.
Sandve, Simen R.
Miller, Jason R.
Kent, Matthew P.
Nome, Torfinn
Hvidsten, Torgeir R.
Leong, Jong S.
Minkley, David R.
Zimin, Aleksey
Grammes, Fabian
Grove, Harald
Gjuvsland, Arne
Walenz, Brian
Hermansen, Russell A.
von Schalburg, Kris
Rondeau, Eric B.
Di Genova, Alex
Samy, Jeevan K. A.
Olav Vik, Jon
Vigeland, Magnus D.
Caler, Lis
Grimholt, Unni
Jentoft, Sissel
Inge Våge, Dag
de Jong, Pieter
Moen, Thomas
Baranski, Matthew
Palti, Yniv
Smith, Douglas R.
Yorke, James A.
Nederbragt, Alexander J.
Tooming-Klunderud, Ave
Jakobsen, Kjetill S.
Jiang, Xuanting
Fan, Dingding
Hu, Yan
Liberles, David A.
Vidal, Rodrigo
Iturra, Patricia
Jones, Steven J. M.
Jonassen, Inge
Maass, Alejandro
Omholt, Stig W.
Davidson, William S.
author_facet Lien, Sigbjørn
Koop, Ben F.
Sandve, Simen R.
Miller, Jason R.
Kent, Matthew P.
Nome, Torfinn
Hvidsten, Torgeir R.
Leong, Jong S.
Minkley, David R.
Zimin, Aleksey
Grammes, Fabian
Grove, Harald
Gjuvsland, Arne
Walenz, Brian
Hermansen, Russell A.
von Schalburg, Kris
Rondeau, Eric B.
Di Genova, Alex
Samy, Jeevan K. A.
Olav Vik, Jon
Vigeland, Magnus D.
Caler, Lis
Grimholt, Unni
Jentoft, Sissel
Inge Våge, Dag
de Jong, Pieter
Moen, Thomas
Baranski, Matthew
Palti, Yniv
Smith, Douglas R.
Yorke, James A.
Nederbragt, Alexander J.
Tooming-Klunderud, Ave
Jakobsen, Kjetill S.
Jiang, Xuanting
Fan, Dingding
Hu, Yan
Liberles, David A.
Vidal, Rodrigo
Iturra, Patricia
Jones, Steven J. M.
Jonassen, Inge
Maass, Alejandro
Omholt, Stig W.
Davidson, William S.
author_sort Lien, Sigbjørn
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users.
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spelling pubmed-81278232021-06-01 The Atlantic salmon genome provides insights into rediploidization Lien, Sigbjørn Koop, Ben F. Sandve, Simen R. Miller, Jason R. Kent, Matthew P. Nome, Torfinn Hvidsten, Torgeir R. Leong, Jong S. Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. Olav Vik, Jon Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Inge Våge, Dag de Jong, Pieter Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas R. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill S. Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. Nature Article 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. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature17164) contains supplementary material, which is available to authorized users. Nature Publishing Group UK 2016-04-18 2016 /pmc/articles/PMC8127823/ /pubmed/27088604 http://dx.doi.org/10.1038/nature17164 Text en © The Author(s) 2016 https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/)
spellingShingle Article
Lien, Sigbjørn
Koop, Ben F.
Sandve, Simen R.
Miller, Jason R.
Kent, Matthew P.
Nome, Torfinn
Hvidsten, Torgeir R.
Leong, Jong S.
Minkley, David R.
Zimin, Aleksey
Grammes, Fabian
Grove, Harald
Gjuvsland, Arne
Walenz, Brian
Hermansen, Russell A.
von Schalburg, Kris
Rondeau, Eric B.
Di Genova, Alex
Samy, Jeevan K. A.
Olav Vik, Jon
Vigeland, Magnus D.
Caler, Lis
Grimholt, Unni
Jentoft, Sissel
Inge Våge, Dag
de Jong, Pieter
Moen, Thomas
Baranski, Matthew
Palti, Yniv
Smith, Douglas R.
Yorke, James A.
Nederbragt, Alexander J.
Tooming-Klunderud, Ave
Jakobsen, Kjetill S.
Jiang, Xuanting
Fan, Dingding
Hu, Yan
Liberles, David A.
Vidal, Rodrigo
Iturra, Patricia
Jones, Steven J. M.
Jonassen, Inge
Maass, Alejandro
Omholt, Stig W.
Davidson, William S.
The Atlantic salmon genome provides insights into rediploidization
title The Atlantic salmon genome provides insights into rediploidization
title_full The Atlantic salmon genome provides insights into rediploidization
title_fullStr The Atlantic salmon genome provides insights into rediploidization
title_full_unstemmed The Atlantic salmon genome provides insights into rediploidization
title_short The Atlantic salmon genome provides insights into rediploidization
title_sort atlantic salmon genome provides insights into rediploidization
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127823/
https://www.ncbi.nlm.nih.gov/pubmed/27088604
http://dx.doi.org/10.1038/nature17164
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