Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication
Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assemblin...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10752349/ http://www.ncbi.nlm.nih.gov/pubmed/38085037 https://doi.org/10.1093/gbe/evad229 |
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ftpubmed:oai:pubmedcentral.nih.gov:10752349 2024-01-28T10:04:04+01:00 Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication Dallaire, Xavier Bouchard, Raphael Hénault, Philippe Ulmo-Diaz, Gabriela Normandeau, Eric Mérot, Claire Bernatchez, Louis Moore, Jean-Sébastien 2023-12-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10752349/ http://www.ncbi.nlm.nih.gov/pubmed/38085037 https://doi.org/10.1093/gbe/evad229 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10752349/ http://www.ncbi.nlm.nih.gov/pubmed/38085037 http://dx.doi.org/10.1093/gbe/evad229 © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Genome Biol Evol Article Text 2023 ftpubmed https://doi.org/10.1093/gbe/evad229 2023-12-31T01:52:09Z Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise F(ST) values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths. Text Arctic Atlantic salmon Salmo salar Salvelinus alpinus PubMed Central (PMC) Arctic Genome Biology and Evolution 15 12 |
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Article Dallaire, Xavier Bouchard, Raphael Hénault, Philippe Ulmo-Diaz, Gabriela Normandeau, Eric Mérot, Claire Bernatchez, Louis Moore, Jean-Sébastien Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication |
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Article |
description |
Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise F(ST) values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths. |
format |
Text |
author |
Dallaire, Xavier Bouchard, Raphael Hénault, Philippe Ulmo-Diaz, Gabriela Normandeau, Eric Mérot, Claire Bernatchez, Louis Moore, Jean-Sébastien |
author_facet |
Dallaire, Xavier Bouchard, Raphael Hénault, Philippe Ulmo-Diaz, Gabriela Normandeau, Eric Mérot, Claire Bernatchez, Louis Moore, Jean-Sébastien |
author_sort |
Dallaire, Xavier |
title |
Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication |
title_short |
Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication |
title_full |
Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication |
title_fullStr |
Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication |
title_full_unstemmed |
Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication |
title_sort |
widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements, and duplication |
publisher |
Oxford University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10752349/ http://www.ncbi.nlm.nih.gov/pubmed/38085037 https://doi.org/10.1093/gbe/evad229 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
genre_facet |
Arctic Atlantic salmon Salmo salar Salvelinus alpinus |
op_source |
Genome Biol Evol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10752349/ http://www.ncbi.nlm.nih.gov/pubmed/38085037 http://dx.doi.org/10.1093/gbe/evad229 |
op_rights |
© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
op_doi |
https://doi.org/10.1093/gbe/evad229 |
container_title |
Genome Biology and Evolution |
container_volume |
15 |
container_issue |
12 |
_version_ |
1789329656704401408 |