Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations

• Published in: Evolutionary Applications
• Main Authors: Lecomte, Laurie, Arnyasi, Mariann, Ferchaud, Anne-Laure, Kent, Matthew, Lien, Sigbjorn, Stenløkk, Kristina, Sylvestre, Florent, Bernatchez, Louis, Mérot, Claire
• Other Authors: Institut de Biologie Intégrative et des Systèmes Québec (IBIS), Norwegian University of Life Sciences (NMBU), Université de Rennes (UR), Ecosystèmes, biodiversité, évolution Rennes (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement - CNRS Ecologie et Environnement (INEE-CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), This project was funded by Société Saumon de la Rivière Romaine, Hydro-Québec, Ressources Aquatiques Québec and by a Collaborative Research and Development grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) to Louis Bernatchez. Laurie Lecomte was supported by a Canada Graduate Scholarship for Master's grant (NSERC) and a master's training scholarship from the Fonds de recherche du Québec – Nature and technologies (FRQNT).
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2024
• Subjects: local adaptation; long‐read sequencing; pangenome; short‐read sequencing; structural variation; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Canada; Indel’; Atlantic salmon; Salmo salar
• Online Access: https://hal.science/hal-04533973; https://hal.science/hal-04533973/document; https://hal.science/hal-04533973/file/Evolutionary%20Applications%20-%202024%20-%20Lecomte%20-%20Investigating%20structural%20variant%20indel%20and%20single%20nucleotide%20polymorphism.pdf; https://doi.org/10.1111/eva.13653

International audience Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-re...