Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection
Background: Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or...
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ftunivbergen:oai:bora.uib.no:1956/15256 2023-05-15T15:32:02+02:00 Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection Kjærner-Semb, Erik Nordtorp Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Vähä, Juha-Pekka Glover, Kevin Rubin, Carl J. Wargelius, Anna Edvardsen, Rolf 2016-11-23T12:16:00Z application/pdf https://hdl.handle.net/1956/15256 https://doi.org/10.1186/s12864-016-2867-z eng eng BioMed Central Norges forskningsråd: 226221 Havforskningsinstituttet: 99411-01 urn:issn:1471-2164 https://hdl.handle.net/1956/15256 https://doi.org/10.1186/s12864-016-2867-z cristin:1402355 Attribution CC BY http://creativecommons.org/licenses/by/4.0 Copyright 2016 The Author(s) Whole genome duplication Adaptation Aquaculture Immune system GWAS Resequencing Selective sweep SNPs Salmo Salar Peer reviewed Journal article 2016 ftunivbergen https://doi.org/10.1186/s12864-016-2867-z 2023-03-14T17:38:59Z Background: Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. Results: In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13–15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Conclusion: Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation. publishedVersion Article in Journal/Newspaper Atlantic salmon Salmo salar University of Bergen: Bergen Open Research Archive (BORA-UiB) Norway BMC Genomics 17 1 |
institution |
Open Polar |
collection |
University of Bergen: Bergen Open Research Archive (BORA-UiB) |
op_collection_id |
ftunivbergen |
language |
English |
topic |
Whole genome duplication Adaptation Aquaculture Immune system GWAS Resequencing Selective sweep SNPs Salmo Salar |
spellingShingle |
Whole genome duplication Adaptation Aquaculture Immune system GWAS Resequencing Selective sweep SNPs Salmo Salar Kjærner-Semb, Erik Nordtorp Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Vähä, Juha-Pekka Glover, Kevin Rubin, Carl J. Wargelius, Anna Edvardsen, Rolf Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
topic_facet |
Whole genome duplication Adaptation Aquaculture Immune system GWAS Resequencing Selective sweep SNPs Salmo Salar |
description |
Background: Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. Results: In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13–15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Conclusion: Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation. publishedVersion |
format |
Article in Journal/Newspaper |
author |
Kjærner-Semb, Erik Nordtorp Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Vähä, Juha-Pekka Glover, Kevin Rubin, Carl J. Wargelius, Anna Edvardsen, Rolf |
author_facet |
Kjærner-Semb, Erik Nordtorp Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Vähä, Juha-Pekka Glover, Kevin Rubin, Carl J. Wargelius, Anna Edvardsen, Rolf |
author_sort |
Kjærner-Semb, Erik Nordtorp |
title |
Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
title_short |
Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
title_full |
Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
title_fullStr |
Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
title_full_unstemmed |
Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
title_sort |
atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
publisher |
BioMed Central |
publishDate |
2016 |
url |
https://hdl.handle.net/1956/15256 https://doi.org/10.1186/s12864-016-2867-z |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
Norges forskningsråd: 226221 Havforskningsinstituttet: 99411-01 urn:issn:1471-2164 https://hdl.handle.net/1956/15256 https://doi.org/10.1186/s12864-016-2867-z cristin:1402355 |
op_rights |
Attribution CC BY http://creativecommons.org/licenses/by/4.0 Copyright 2016 The Author(s) |
op_doi |
https://doi.org/10.1186/s12864-016-2867-z |
container_title |
BMC Genomics |
container_volume |
17 |
container_issue |
1 |
_version_ |
1766362533676974080 |