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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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Autores principales: Hale, Matthew C, Campbell, Matthew A, McKinney, Garrett J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473973/
https://www.ncbi.nlm.nih.gov/pubmed/34568922
http://dx.doi.org/10.1093/g3journal/jkab267
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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
collection PubMed
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.
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spelling pubmed-84739732021-09-27 A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques Hale, Matthew C Campbell, Matthew A McKinney, Garrett J G3 (Bethesda) Investigation 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. Oxford University Press 2021-07-28 /pmc/articles/PMC8473973/ /pubmed/34568922 http://dx.doi.org/10.1093/g3journal/jkab267 Text en © 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.
spellingShingle 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
title 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_short 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
topic Investigation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8473973/
https://www.ncbi.nlm.nih.gov/pubmed/34568922
http://dx.doi.org/10.1093/g3journal/jkab267
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