Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection
Abstract 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 influe...
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ftdatacite:10.6084/m9.figshare.c.3598010 2023-05-15T15:32:10+02:00 Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection Kjærner-Semb, Erik Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Juha-Pekka Vähä Glover, Kevin Rubin, Carl Wargelius, Anna Edvardsen, Rolf 2016 https://dx.doi.org/10.6084/m9.figshare.c.3598010 https://figshare.com/collections/Atlantic_salmon_populations_reveal_adaptive_divergence_of_immune_related_genes_-_a_duplicated_genome_under_selection/3598010 unknown Figshare https://dx.doi.org/10.1186/s12864-016-2867-z CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Cell Biology Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences Collection article 2016 ftdatacite https://doi.org/10.6084/m9.figshare.c.3598010 https://doi.org/10.1186/s12864-016-2867-z 2021-11-05T12:55:41Z Abstract 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. Article in Journal/Newspaper Atlantic salmon DataCite Metadata Store (German National Library of Science and Technology) Norway |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Cell Biology Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences |
spellingShingle |
Cell Biology Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences Kjærner-Semb, Erik Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Juha-Pekka Vähä Glover, Kevin Rubin, Carl Wargelius, Anna Edvardsen, Rolf Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection |
topic_facet |
Cell Biology Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology 110309 Infectious Diseases FOS Health sciences |
description |
Abstract 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. |
format |
Article in Journal/Newspaper |
author |
Kjærner-Semb, Erik Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Juha-Pekka Vähä Glover, Kevin Rubin, Carl Wargelius, Anna Edvardsen, Rolf |
author_facet |
Kjærner-Semb, Erik Ayllon, Fernando Furmanek, Tomasz Wennevik, Vidar Dahle, Geir Niemelä, Eero Ozerov, Mikhail Juha-Pekka Vähä Glover, Kevin Rubin, Carl Wargelius, Anna Edvardsen, Rolf |
author_sort |
Kjærner-Semb, Erik |
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 |
Figshare |
publishDate |
2016 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3598010 https://figshare.com/collections/Atlantic_salmon_populations_reveal_adaptive_divergence_of_immune_related_genes_-_a_duplicated_genome_under_selection/3598010 |
geographic |
Norway |
geographic_facet |
Norway |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
https://dx.doi.org/10.1186/s12864-016-2867-z |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3598010 https://doi.org/10.1186/s12864-016-2867-z |
_version_ |
1766362675042844672 |