Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations
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...
Published in: | Evolutionary Applications |
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Main Authors: | , , , , , , , , |
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Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2024
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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 |
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Université de Rennes 1: Publications scientifiques (HAL) |
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ftunivrennes1hal |
language |
English |
topic |
local adaptation long‐read sequencing pangenome short‐read sequencing structural variation [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
local adaptation long‐read sequencing pangenome short‐read sequencing structural variation [SDE.BE]Environmental Sciences/Biodiversity and Ecology Lecomte, Laurie Arnyasi, Mariann Ferchaud, Anne-Laure Kent, Matthew Lien, Sigbjorn Stenløkk, Kristina Sylvestre, Florent Bernatchez, Louis Mérot, Claire Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations |
topic_facet |
local adaptation long‐read sequencing pangenome short‐read sequencing structural variation [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
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-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F (ST) and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore ... |
author2 |
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 |
author |
Lecomte, Laurie Arnyasi, Mariann Ferchaud, Anne-Laure Kent, Matthew Lien, Sigbjorn Stenløkk, Kristina Sylvestre, Florent Bernatchez, Louis Mérot, Claire |
author_facet |
Lecomte, Laurie Arnyasi, Mariann Ferchaud, Anne-Laure Kent, Matthew Lien, Sigbjorn Stenløkk, Kristina Sylvestre, Florent Bernatchez, Louis Mérot, Claire |
author_sort |
Lecomte, Laurie |
title |
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations |
title_short |
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations |
title_full |
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations |
title_fullStr |
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations |
title_full_unstemmed |
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations |
title_sort |
investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted atlantic salmon populations |
publisher |
HAL CCSD |
publishDate |
2024 |
url |
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 |
long_lat |
ENVELOPE(35.282,35.282,66.963,66.963) |
geographic |
Canada Indel’ |
geographic_facet |
Canada Indel’ |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
ISSN: 1752-4571 Evolutionary Applications https://hal.science/hal-04533973 Evolutionary Applications, 2024, 17 (3), pp.e13653. ⟨10.1111/eva.13653⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/eva.13653 info:eu-repo/semantics/altIdentifier/pmid/38495945 hal-04533973 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 doi:10.1111/eva.13653 PUBMED: 38495945 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1111/eva.13653 |
container_title |
Evolutionary Applications |
container_volume |
17 |
container_issue |
3 |
_version_ |
1798843436130893824 |
spelling |
ftunivrennes1hal:oai:HAL:hal-04533973v1 2024-05-12T08:01:19+00:00 Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations Lecomte, Laurie Arnyasi, Mariann Ferchaud, Anne-Laure Kent, Matthew Lien, Sigbjorn Stenløkk, Kristina Sylvestre, Florent Bernatchez, Louis Mérot, Claire 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). 2024-03 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 en eng HAL CCSD info:eu-repo/semantics/altIdentifier/doi/10.1111/eva.13653 info:eu-repo/semantics/altIdentifier/pmid/38495945 hal-04533973 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 doi:10.1111/eva.13653 PUBMED: 38495945 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1752-4571 Evolutionary Applications https://hal.science/hal-04533973 Evolutionary Applications, 2024, 17 (3), pp.e13653. ⟨10.1111/eva.13653⟩ local adaptation long‐read sequencing pangenome short‐read sequencing structural variation [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2024 ftunivrennes1hal https://doi.org/10.1111/eva.13653 2024-04-18T00:06:14Z 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-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F (ST) and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore ... Article in Journal/Newspaper Atlantic salmon Salmo salar Université de Rennes 1: Publications scientifiques (HAL) Canada Indel’ ENVELOPE(35.282,35.282,66.963,66.963) Evolutionary Applications 17 3 |