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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Umeå universitet, Institutionen för fysiologisk botanik
2016
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-121444 https://doi.org/10.1038/nature17164 |
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ftumeauniv:oai:DiVA.org:umu-121444 2023-10-09T21:49:54+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, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. 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, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. 2016 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-121444 https://doi.org/10.1038/nature17164 eng eng Umeå universitet, Institutionen för fysiologisk botanik Umeå universitet, Umeå Plant Science Centre (UPSC) Nature, 0028-0836, 2016, 533:7602, s. 200-205 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-121444 doi:10.1038/nature17164 PMID 27088604 ISI:000376007200040 Scopus 2-s2.0-84969136024 info:eu-repo/semantics/openAccess Biological Sciences Biologiska vetenskaper Article in journal info:eu-repo/semantics/article text 2016 ftumeauniv https://doi.org/10.1038/nature17164 2023-09-22T13:58:30Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Umeå University: Publications (DiVA) Nature 533 7602 200 205 |
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Open Polar |
collection |
Umeå University: Publications (DiVA) |
op_collection_id |
ftumeauniv |
language |
English |
topic |
Biological Sciences Biologiska vetenskaper |
spellingShingle |
Biological Sciences Biologiska vetenskaper 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, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. 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, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. The Atlantic salmon genome provides insights into rediploidization |
topic_facet |
Biological Sciences Biologiska vetenskaper |
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. |
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, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. 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, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. |
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, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. 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, Patricia Jones, Steven J. M. Jonassen, Inge Maass, 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 |
Umeå universitet, Institutionen för fysiologisk botanik |
publishDate |
2016 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-121444 https://doi.org/10.1038/nature17164 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Nature, 0028-0836, 2016, 533:7602, s. 200-205 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-121444 doi:10.1038/nature17164 PMID 27088604 ISI:000376007200040 Scopus 2-s2.0-84969136024 |
op_rights |
info:eu-repo/semantics/openAccess |
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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1779312948067434496 |