A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques
The “genomics era” has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy numb...
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ftpubmed:oai:pubmedcentral.nih.gov:8473973 2023-05-15T14:30:04+02:00 A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques Hale, Matthew C Campbell, Matthew A McKinney, Garrett J 2021-07-28 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473973/ http://www.ncbi.nlm.nih.gov/pubmed/34568922 https://doi.org/10.1093/g3journal/jkab267 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473973/ http://www.ncbi.nlm.nih.gov/pubmed/34568922 http://dx.doi.org/10.1093/g3journal/jkab267 © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY G3 (Bethesda) Investigation Text 2021 ftpubmed https://doi.org/10.1093/g3journal/jkab267 2021-10-03T01:17:06Z The “genomics era” has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr—one each from Nunavut, Newfoundland, Eastern Russia, and Scotland—and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved. Text Arctic charr Arctic Newfoundland Nunavut Salvelinus alpinus PubMed Central (PMC) Arctic Canada Nunavut G3 Genes|Genomes|Genetics 11 10 |
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English |
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Investigation |
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Investigation Hale, Matthew C Campbell, Matthew A McKinney, Garrett J A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques |
topic_facet |
Investigation |
description |
The “genomics era” has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr—one each from Nunavut, Newfoundland, Eastern Russia, and Scotland—and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved. |
format |
Text |
author |
Hale, Matthew C Campbell, Matthew A McKinney, Garrett J |
author_facet |
Hale, Matthew C Campbell, Matthew A McKinney, Garrett J |
author_sort |
Hale, Matthew C |
title |
A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques |
title_short |
A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques |
title_full |
A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques |
title_fullStr |
A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques |
title_full_unstemmed |
A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques |
title_sort |
candidate chromosome inversion in arctic charr (salvelinus alpinus) identified by population genetic analysis techniques |
publisher |
Oxford University Press |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473973/ http://www.ncbi.nlm.nih.gov/pubmed/34568922 https://doi.org/10.1093/g3journal/jkab267 |
geographic |
Arctic Canada Nunavut |
geographic_facet |
Arctic Canada Nunavut |
genre |
Arctic charr Arctic Newfoundland Nunavut Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Newfoundland Nunavut Salvelinus alpinus |
op_source |
G3 (Bethesda) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473973/ http://www.ncbi.nlm.nih.gov/pubmed/34568922 http://dx.doi.org/10.1093/g3journal/jkab267 |
op_rights |
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1093/g3journal/jkab267 |
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G3 Genes|Genomes|Genetics |
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11 |
container_issue |
10 |
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1766303995778826240 |