The structural variation landscape in 492 Atlantic salmon genomes.

Autor:	Bertolotti AC; School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, UK.; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK., Layer RM; BioFrontiers Institute, University of Colorado, Boulder, CO, USA.; Department of Computer Science, University of Colorado, Boulder, CO, USA., Gundappa MK; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK., Gallagher MD; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK., Pehlivanoglu E; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK., Nome T; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., Robledo D; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK., Kent MP; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., Røsæg LL; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., Holen MM; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., Mulugeta TD; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., Ashton TJ; Xelect Ltd, Horizon House, St Andrews, UK., Hindar K; Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway., Sægrov H; Rådgivende Biologer AS, Bergen, Norway., Florø-Larsen B; Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway., Erkinaro J; Natural Resources Institute Finland (Luke), P.O. Box 413, FI-90014, Oulu, Finland., Primmer CR; Institute for Biotechnology, University of Helsinki, Helsinki, Finland., Bernatchez L; Institut de Biologie Intégrative et des Systèmes (IBIS) Pavillon Charles-Eugène Marchand, Université Laval Québec, Québec, QC, Canada., Martin SAM; School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen, UK., Johnston IA; Xelect Ltd, Horizon House, St Andrews, UK., Sandve SR; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., Lien S; Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway. sigbjorn.lien@nmbu.no., Macqueen DJ; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK. daniel.macqueen@roslin.ed.ac.uk.
Jazyk:	angličtina
Zdroj:	Nature communications [Nat Commun] 2020 Oct 14; Vol. 11 (1), pp. 5176. Date of Electronic Publication: 2020 Oct 14.
DOI:	10.1038/s41467-020-18972-x
Abstrakt:	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.
Databáze:	MEDLINE
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