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 number...
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fttexaschristuni:oai:repository.tcu.edu:116099117/49932 2023-11-05T03:38:00+01:00 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 https://repository.tcu.edu/handle/116099117/49932 https://doi.org/10.1093/g3journal/jkab267 en eng Oxford Univ Press Inc https://doi.org/10.1093/g3journal/jkab267 https://repository.tcu.edu/handle/116099117/49932 https://creativecommons.org/licenses/by/4.0/ 2021 Authors CC BY 4.0 G3: Genes, Genomes, Genetics chromosomal inversion salmonids population genomics RAD-seq structural variants Article 2021 fttexaschristuni https://doi.org/10.1093/g3journal/jkab267 2023-10-07T22:09:31Z 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 similar to 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. Article in Journal/Newspaper Arctic charr Arctic Newfoundland Nunavut Salvelinus alpinus TCU Digital Repository (Texas Christian University) G3 Genes|Genomes|Genetics 11 10 |
institution |
Open Polar |
collection |
TCU Digital Repository (Texas Christian University) |
op_collection_id |
fttexaschristuni |
language |
English |
topic |
chromosomal inversion salmonids population genomics RAD-seq structural variants |
spellingShingle |
chromosomal inversion salmonids population genomics RAD-seq structural variants 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 |
chromosomal inversion salmonids population genomics RAD-seq structural variants |
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 similar to 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 |
Article in Journal/Newspaper |
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 Univ Press Inc |
publishDate |
2021 |
url |
https://repository.tcu.edu/handle/116099117/49932 https://doi.org/10.1093/g3journal/jkab267 |
genre |
Arctic charr Arctic Newfoundland Nunavut Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Newfoundland Nunavut Salvelinus alpinus |
op_source |
G3: Genes, Genomes, Genetics |
op_relation |
https://doi.org/10.1093/g3journal/jkab267 https://repository.tcu.edu/handle/116099117/49932 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ 2021 Authors CC BY 4.0 |
op_doi |
https://doi.org/10.1093/g3journal/jkab267 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
11 |
container_issue |
10 |
_version_ |
1781693708382502912 |