A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occu...
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ftpubmed:oai:pubmedcentral.nih.gov:5295600 2023-05-15T14:30:02+02:00 A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication Nugent, Cameron M. Easton, Anne A. Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. 2016-12-16 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295600/ http://www.ncbi.nlm.nih.gov/pubmed/27986793 https://doi.org/10.1534/g3.116.038026 en eng Genetics Society of America http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295600/ http://www.ncbi.nlm.nih.gov/pubmed/27986793 http://dx.doi.org/10.1534/g3.116.038026 Copyright © 2017 Nugent et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY Investigations Text 2016 ftpubmed https://doi.org/10.1534/g3.116.038026 2017-02-12T01:14:58Z Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions. Text Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus PubMed Central (PMC) Arctic G3 Genes|Genomes|Genetics 7 2 543 556 |
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English |
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Investigations |
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Investigations Nugent, Cameron M. Easton, Anne A. Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
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Investigations |
description |
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions. |
format |
Text |
author |
Nugent, Cameron M. Easton, Anne A. Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. |
author_facet |
Nugent, Cameron M. Easton, Anne A. Norman, Joseph D. Ferguson, Moira M. Danzmann, Roy G. |
author_sort |
Nugent, Cameron M. |
title |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_short |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_full |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_fullStr |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_full_unstemmed |
A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication |
title_sort |
snp based linkage map of the arctic charr (salvelinus alpinus) genome provides insights into the diploidization process after whole genome duplication |
publisher |
Genetics Society of America |
publishDate |
2016 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295600/ http://www.ncbi.nlm.nih.gov/pubmed/27986793 https://doi.org/10.1534/g3.116.038026 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295600/ http://www.ncbi.nlm.nih.gov/pubmed/27986793 http://dx.doi.org/10.1534/g3.116.038026 |
op_rights |
Copyright © 2017 Nugent et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.116.038026 |
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G3 Genes|Genomes|Genetics |
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7 |
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2 |
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543 |
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556 |
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