The structural variation landscape in 492 Atlantic salmon genomes
Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-c...
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ftpubmed:oai:pubmedcentral.nih.gov:7560756 2023-05-15T15:30:49+02:00 The structural variation landscape in 492 Atlantic salmon genomes Bertolotti, Alicia C. Layer, Ryan M. Gundappa, Manu Kumar Gallagher, Michael D. Pehlivanoglu, Ege Nome, Torfinn Robledo, Diego Kent, Matthew P. Røsæg, Line L. Holen, Matilde M. Mulugeta, Teshome D. Ashton, Thomas J. Hindar, Kjetil Sægrov, Harald Florø-Larsen, Bjørn Erkinaro, Jaakko Primmer, Craig R. Bernatchez, Louis Martin, Samuel A. M. Johnston, Ian A. Sandve, Simen R. Lien, Sigbjørn Macqueen, Daniel J. 2020-10-14 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560756/ http://www.ncbi.nlm.nih.gov/pubmed/33056985 https://doi.org/10.1038/s41467-020-18972-x en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560756/ http://www.ncbi.nlm.nih.gov/pubmed/33056985 http://dx.doi.org/10.1038/s41467-020-18972-x © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. CC-BY Nat Commun Article Text 2020 ftpubmed https://doi.org/10.1038/s41467-020-18972-x 2020-10-25T00:40:18Z Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species. Text Atlantic salmon Salmo salar PubMed Central (PMC) Nature Communications 11 1 |
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Article Bertolotti, Alicia C. Layer, Ryan M. Gundappa, Manu Kumar Gallagher, Michael D. Pehlivanoglu, Ege Nome, Torfinn Robledo, Diego Kent, Matthew P. Røsæg, Line L. Holen, Matilde M. Mulugeta, Teshome D. Ashton, Thomas J. Hindar, Kjetil Sægrov, Harald Florø-Larsen, Bjørn Erkinaro, Jaakko Primmer, Craig R. Bernatchez, Louis Martin, Samuel A. M. Johnston, Ian A. Sandve, Simen R. Lien, Sigbjørn Macqueen, Daniel J. The structural variation landscape in 492 Atlantic salmon genomes |
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description |
Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species. |
format |
Text |
author |
Bertolotti, Alicia C. Layer, Ryan M. Gundappa, Manu Kumar Gallagher, Michael D. Pehlivanoglu, Ege Nome, Torfinn Robledo, Diego Kent, Matthew P. Røsæg, Line L. Holen, Matilde M. Mulugeta, Teshome D. Ashton, Thomas J. Hindar, Kjetil Sægrov, Harald Florø-Larsen, Bjørn Erkinaro, Jaakko Primmer, Craig R. Bernatchez, Louis Martin, Samuel A. M. Johnston, Ian A. Sandve, Simen R. Lien, Sigbjørn Macqueen, Daniel J. |
author_facet |
Bertolotti, Alicia C. Layer, Ryan M. Gundappa, Manu Kumar Gallagher, Michael D. Pehlivanoglu, Ege Nome, Torfinn Robledo, Diego Kent, Matthew P. Røsæg, Line L. Holen, Matilde M. Mulugeta, Teshome D. Ashton, Thomas J. Hindar, Kjetil Sægrov, Harald Florø-Larsen, Bjørn Erkinaro, Jaakko Primmer, Craig R. Bernatchez, Louis Martin, Samuel A. M. Johnston, Ian A. Sandve, Simen R. Lien, Sigbjørn Macqueen, Daniel J. |
author_sort |
Bertolotti, Alicia C. |
title |
The structural variation landscape in 492 Atlantic salmon genomes |
title_short |
The structural variation landscape in 492 Atlantic salmon genomes |
title_full |
The structural variation landscape in 492 Atlantic salmon genomes |
title_fullStr |
The structural variation landscape in 492 Atlantic salmon genomes |
title_full_unstemmed |
The structural variation landscape in 492 Atlantic salmon genomes |
title_sort |
structural variation landscape in 492 atlantic salmon genomes |
publisher |
Nature Publishing Group UK |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560756/ http://www.ncbi.nlm.nih.gov/pubmed/33056985 https://doi.org/10.1038/s41467-020-18972-x |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Nat Commun |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560756/ http://www.ncbi.nlm.nih.gov/pubmed/33056985 http://dx.doi.org/10.1038/s41467-020-18972-x |
op_rights |
© The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41467-020-18972-x |
container_title |
Nature Communications |
container_volume |
11 |
container_issue |
1 |
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1766361278423498752 |