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...
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Online Access: | https://hdl.handle.net/1956/17363 https://doi.org/10.1038/nature17164 |
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ftunivbergen:oai:bora.uib.no:1956/17363 2023-05-15T15:30:21+02:00 The Atlantic salmon genome provides insights into rediploidization Lien, Sigbjørn Koop, Ben F Sandve, Simen Rød Miller, Jason R. Kent, Matthew Peter Nome, Torfinn Hvidsten, Torgeir Rhoden Leong, Jong Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Bjørke Walenz, Brian Hermansen, Russell A. von Schalburg, Kristian R. Rondeau, Eric Genova, Alex Di Antony Samy, Jeevan Karloss Vik, Jon Olav Vigeland, Magnus Dehli Caler, Lis Grimholt, Unni Jentoft, Sissel Våge, Dag Inge de Jong, Pieter J. Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas W. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill Sigurd Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J.M. Jonassen, Inge Maass, Alejandro Omholt, Stig William Davidson, William S 2018-01-30T10:25:57Z application/pdf https://hdl.handle.net/1956/17363 https://doi.org/10.1038/nature17164 eng eng Nature Publishing Group Norges forskningsråd: 222378 Norges forskningsråd: 179569 urn:issn:1476-4687 urn:issn:0028-0836 https://hdl.handle.net/1956/17363 https://doi.org/10.1038/nature17164 cristin:1357548 Attribution CC BY http://creativecommons.org/licenses/by/4.0 Copyright 2016 The Author(s) Nature Peer reviewed Journal article 2018 ftunivbergen https://doi.org/10.1038/nature17164 2023-03-14T17:44:33Z 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. publishedVersion Article in Journal/Newspaper Atlantic salmon Salmo salar University of Bergen: Bergen Open Research Archive (BORA-UiB) Nature 533 7602 200 205 |
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Open Polar |
collection |
University of Bergen: Bergen Open Research Archive (BORA-UiB) |
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ftunivbergen |
language |
English |
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. publishedVersion |
format |
Article in Journal/Newspaper |
author |
Lien, Sigbjørn Koop, Ben F Sandve, Simen Rød Miller, Jason R. Kent, Matthew Peter Nome, Torfinn Hvidsten, Torgeir Rhoden Leong, Jong Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Bjørke Walenz, Brian Hermansen, Russell A. von Schalburg, Kristian R. Rondeau, Eric Genova, Alex Di Antony Samy, Jeevan Karloss Vik, Jon Olav Vigeland, Magnus Dehli Caler, Lis Grimholt, Unni Jentoft, Sissel Våge, Dag Inge de Jong, Pieter J. Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas W. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill Sigurd Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J.M. Jonassen, Inge Maass, Alejandro Omholt, Stig William Davidson, William S |
spellingShingle |
Lien, Sigbjørn Koop, Ben F Sandve, Simen Rød Miller, Jason R. Kent, Matthew Peter Nome, Torfinn Hvidsten, Torgeir Rhoden Leong, Jong Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Bjørke Walenz, Brian Hermansen, Russell A. von Schalburg, Kristian R. Rondeau, Eric Genova, Alex Di Antony Samy, Jeevan Karloss Vik, Jon Olav Vigeland, Magnus Dehli Caler, Lis Grimholt, Unni Jentoft, Sissel Våge, Dag Inge de Jong, Pieter J. Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas W. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill Sigurd Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J.M. Jonassen, Inge Maass, Alejandro Omholt, Stig William Davidson, William S The Atlantic salmon genome provides insights into rediploidization |
author_facet |
Lien, Sigbjørn Koop, Ben F Sandve, Simen Rød Miller, Jason R. Kent, Matthew Peter Nome, Torfinn Hvidsten, Torgeir Rhoden Leong, Jong Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Bjørke Walenz, Brian Hermansen, Russell A. von Schalburg, Kristian R. Rondeau, Eric Genova, Alex Di Antony Samy, Jeevan Karloss Vik, Jon Olav Vigeland, Magnus Dehli Caler, Lis Grimholt, Unni Jentoft, Sissel Våge, Dag Inge de Jong, Pieter J. Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas W. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill Sigurd Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J.M. Jonassen, Inge Maass, Alejandro Omholt, Stig William Davidson, William S |
author_sort |
Lien, Sigbjørn |
title |
The Atlantic salmon genome provides insights into rediploidization |
title_short |
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_sort |
atlantic salmon genome provides insights into rediploidization |
publisher |
Nature Publishing Group |
publishDate |
2018 |
url |
https://hdl.handle.net/1956/17363 https://doi.org/10.1038/nature17164 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Nature |
op_relation |
Norges forskningsråd: 222378 Norges forskningsråd: 179569 urn:issn:1476-4687 urn:issn:0028-0836 https://hdl.handle.net/1956/17363 https://doi.org/10.1038/nature17164 cristin:1357548 |
op_rights |
Attribution CC BY http://creativecommons.org/licenses/by/4.0 Copyright 2016 The Author(s) |
op_doi |
https://doi.org/10.1038/nature17164 |
container_title |
Nature |
container_volume |
533 |
container_issue |
7602 |
container_start_page |
200 |
op_container_end_page |
205 |
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1766360802336440320 |