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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ftunivmob:oai:nmbu.brage.unit.no:11250/2687416 2023-05-15T15:30:59+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 Peter Røsæg, Line Lieblein Holen, Matilde Mengkrog Mulugeta, Teshome Dagne 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 Rød Lien, Sigbjørn Macqueen, Daniel J. 2020-10-14T14:32:00Z application/pdf https://hdl.handle.net/11250/2687416 https://doi.org/10.1038/s41467-020-18972-x eng eng Norges forskningsråd: 221734 Nature Communications, 2020, 11, Article number: 5176 urn:issn:2041-1723 https://hdl.handle.net/11250/2687416 https://doi.org/10.1038/s41467-020-18972-x cristin:1839588 Attribution-NonCommercial-NoDerivatives 4.0 Internasjonal http://creativecommons.org/licenses/by-nc-nd/4.0/deed.no CC-BY-NC-ND 11 Nature Communications 5176 VDP::Klinisk veterinærmedisinske fag: 950 VDP::Clinical veterinary sciences: 950 Peer reviewed Journal article 2020 ftunivmob https://doi.org/10.1038/s41467-020-18972-x 2021-09-23T20:15:09Z 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. publishedVersion Article in Journal/Newspaper Atlantic salmon Salmo salar Open archive Norwegian University of Life Sciences: Brage NMBU Nature Communications 11 1 |
institution |
Open Polar |
collection |
Open archive Norwegian University of Life Sciences: Brage NMBU |
op_collection_id |
ftunivmob |
language |
English |
topic |
VDP::Klinisk veterinærmedisinske fag: 950 VDP::Clinical veterinary sciences: 950 |
spellingShingle |
VDP::Klinisk veterinærmedisinske fag: 950 VDP::Clinical veterinary sciences: 950 Bertolotti, Alicia C. Layer, Ryan M. Gundappa, Manu Kumar Gallagher, Michael D. Pehlivanoglu, Ege Nome, Torfinn Robledo, Diego Kent, Matthew Peter Røsæg, Line Lieblein Holen, Matilde Mengkrog Mulugeta, Teshome Dagne 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 Rød Lien, Sigbjørn Macqueen, Daniel J. The structural variation landscape in 492 Atlantic salmon genomes |
topic_facet |
VDP::Klinisk veterinærmedisinske fag: 950 VDP::Clinical veterinary sciences: 950 |
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. publishedVersion |
format |
Article in Journal/Newspaper |
author |
Bertolotti, Alicia C. Layer, Ryan M. Gundappa, Manu Kumar Gallagher, Michael D. Pehlivanoglu, Ege Nome, Torfinn Robledo, Diego Kent, Matthew Peter Røsæg, Line Lieblein Holen, Matilde Mengkrog Mulugeta, Teshome Dagne 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 Rød 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 Peter Røsæg, Line Lieblein Holen, Matilde Mengkrog Mulugeta, Teshome Dagne 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 Rød 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 |
publishDate |
2020 |
url |
https://hdl.handle.net/11250/2687416 https://doi.org/10.1038/s41467-020-18972-x |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
11 Nature Communications 5176 |
op_relation |
Norges forskningsråd: 221734 Nature Communications, 2020, 11, Article number: 5176 urn:issn:2041-1723 https://hdl.handle.net/11250/2687416 https://doi.org/10.1038/s41467-020-18972-x cristin:1839588 |
op_rights |
Attribution-NonCommercial-NoDerivatives 4.0 Internasjonal http://creativecommons.org/licenses/by-nc-nd/4.0/deed.no |
op_rightsnorm |
CC-BY-NC-ND |
op_doi |
https://doi.org/10.1038/s41467-020-18972-x |
container_title |
Nature Communications |
container_volume |
11 |
container_issue |
1 |
_version_ |
1766361470215389184 |