The Atlantic salmon genome provides insights into rediploidization
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 hig...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2016
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Materias: | |
Acceso en línea: | 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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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. |
format | Online Article Text |
id | pubmed-8127823 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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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