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://doi.org/10.1038/nature17164 https://repositorio.uchile.cl/handle/2250/140938 |
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ftunivchile:oai:repositorio.uchile.cl:2250/140938 2023-05-15T15:30:44+02:00 The Atlantic salmon genome provides insights into rediploidization Lien, Sigbjorn 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, Fabián Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan Vik, Jon Olav Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Vage, Dag Inge 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 Liberles, David A. Vidal, Rodrigo Iturra Constant, Patricia Jones, Steven J. Jonassen, Inge Maass Sepúlveda, Alejandro Omholt, Stig W. Davidson, William S. 2016 application/pdf https://doi.org/10.1038/nature17164 https://repositorio.uchile.cl/handle/2250/140938 en eng Nature Nature %7C Vol 533 %7C 12 May 2016 doi:10.1038/nature17164 https://repositorio.uchile.cl/handle/2250/140938 Attribution-NonCommercial-NoDerivs 3.0 Chile http://creativecommons.org/licenses/by-nc-nd/3.0/cl/ CC-BY-NC-ND Nature Artículo de revista 2016 ftunivchile https://doi.org/10.1038/nature17164 2023-01-22T00:53:26Z 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. Research Council of Norway (NFR) Norwegian Seafood Research Fund Genome BC Chilean Economic Development Agency - CORFO and InnovaChile Committee Marine Harvest AquaGen Cermaq Salmobreed NFR 208481/F50 226266 225181 221734/030 Natural Sciences and Engineering Research Council (NSERC), Canada University of Victoria Article in Journal/Newspaper Atlantic salmon Salmo salar Universidad de Chile: Repositorio académico Canada Norway Nature 533 7602 200 205 |
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Open Polar |
collection |
Universidad de Chile: Repositorio académico |
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ftunivchile |
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. Research Council of Norway (NFR) Norwegian Seafood Research Fund Genome BC Chilean Economic Development Agency - CORFO and InnovaChile Committee Marine Harvest AquaGen Cermaq Salmobreed NFR 208481/F50 226266 225181 221734/030 Natural Sciences and Engineering Research Council (NSERC), Canada University of Victoria |
format |
Article in Journal/Newspaper |
author |
Lien, Sigbjorn 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, Fabián Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan Vik, Jon Olav Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Vage, Dag Inge 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 Liberles, David A. Vidal, Rodrigo Iturra Constant, Patricia Jones, Steven J. Jonassen, Inge Maass Sepúlveda, Alejandro Omholt, Stig W. Davidson, William S. |
spellingShingle |
Lien, Sigbjorn 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, Fabián Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan Vik, Jon Olav Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Vage, Dag Inge 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 Liberles, David A. Vidal, Rodrigo Iturra Constant, Patricia Jones, Steven J. Jonassen, Inge Maass Sepúlveda, Alejandro Omholt, Stig W. Davidson, William S. The Atlantic salmon genome provides insights into rediploidization |
author_facet |
Lien, Sigbjorn 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, Fabián Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan Vik, Jon Olav Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Vage, Dag Inge 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 Liberles, David A. Vidal, Rodrigo Iturra Constant, Patricia Jones, Steven J. Jonassen, Inge Maass Sepúlveda, Alejandro Omholt, Stig W. Davidson, William S. |
author_sort |
Lien, Sigbjorn |
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 |
publishDate |
2016 |
url |
https://doi.org/10.1038/nature17164 https://repositorio.uchile.cl/handle/2250/140938 |
geographic |
Canada Norway |
geographic_facet |
Canada Norway |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Nature |
op_relation |
Nature %7C Vol 533 %7C 12 May 2016 doi:10.1038/nature17164 https://repositorio.uchile.cl/handle/2250/140938 |
op_rights |
Attribution-NonCommercial-NoDerivs 3.0 Chile http://creativecommons.org/licenses/by-nc-nd/3.0/cl/ |
op_rightsnorm |
CC-BY-NC-ND |
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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1766361196958580736 |