Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS)
Disease emergence is accelerating in response to human activity-induced global changes. Understanding the mechanisms by which host populations can rapidly adapt to this threat will be crucial for developing future management practices. Pacific Oyster Mortality Syndrome (POMS) imposes a substantial a...
Main Authors: | , , , , , , , , , , , , , , , , , , , |
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Other Authors: | , , , , , , , , , , , , , , , , , , |
Format: | Report |
Language: | English |
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HAL CCSD
2024
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Subjects: | |
Online Access: | https://hal.science/hal-04651019 https://hal.science/hal-04651019/document https://hal.science/hal-04651019/file/Gawra-2023-BIORXIV.pdf https://doi.org/10.1101/2023.03.09.531494 |
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ftunivpolynesief:oai:HAL:hal-04651019v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Université de la Polynésie française (upf): HAL |
op_collection_id |
ftunivpolynesief |
language |
English |
topic |
rapid adaptation genetic epigenetic POMS oyster exome capture [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity |
spellingShingle |
rapid adaptation genetic epigenetic POMS oyster exome capture [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity Gawra, Janan Valdivieso, Alejandro Roux, Fabrice Laporte, Martin de Lorgeril, Julien Gueguen, Yannick Saccas, Mathilde Escoubas, Jean-Michel Montagnani, C. Destoumieux-Garzon, Delphine Lagarde, Franck Leroy, Marc, A Haffner, Philippe Petton, Bruno Cosseau, Celine Morga, Benjamin Dégremont, Lionel Mitta, Guillaume Grunau, Christoph Vidal-Dupiol, Jeremie Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) |
topic_facet |
rapid adaptation genetic epigenetic POMS oyster exome capture [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity |
description |
Disease emergence is accelerating in response to human activity-induced global changes. Understanding the mechanisms by which host populations can rapidly adapt to this threat will be crucial for developing future management practices. Pacific Oyster Mortality Syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations ( Crassostrea gigas) . Rapid adaptation to this disease may arise through both genetic and epigenetic mechanisms. In this study, we used a combination of whole exome capture of bisulfite-converted DNA, next-generation sequencing, and (epi)genome-wide association mapping, to show that natural oyster populations differentially exposed to POMS displayed signatures of selection both in their genome (single nucleotide polymorphisms) and epigenome (CG-context DNA methylation). Consistent with higher resistance to POMS, the genes targeted by genetic and epigenetic variations were mainly related to host immunity. By combining correlation analyses, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of the observed phenotypic variation was explained by interactions between the genetic sequence and epigenetic information, ∼14% by the genetic sequence, and up to 25% by the epigenome alone. Thus, as well as genetic adaptation, epigenetic mechanisms governing immune responses contribute significantly to the rapid adaptation of hosts to emerging infectious diseases. |
author2 |
Interactions Hôtes-Pathogènes-Environnements (IHPE) Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) Ministère de l'environnement Ministère de l'Environnement Laboratoire des Interactions Plantes Microbes Environnement (LIPME) Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE Nouvelle-Calédonie ) Institut de Recherche pour le Développement (IRD Nouvelle-Calédonie )-Délégation Ifremer de Nouvelle-Calédonie Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC)-Centre National de la Recherche Scientifique (CNRS) MARine Biodiversity Exploitation and Conservation - MARBEC (UMR MARBEC ) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Unité Adaptation et Santé des Invertébrés Marins (ASIM) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Ecosystèmes Insulaires Océaniens (UMR 241) (EIO) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé Papeete (ILM) Institut de Recherche pour le Développement (IRD) |
format |
Report |
author |
Gawra, Janan Valdivieso, Alejandro Roux, Fabrice Laporte, Martin de Lorgeril, Julien Gueguen, Yannick Saccas, Mathilde Escoubas, Jean-Michel Montagnani, C. Destoumieux-Garzon, Delphine Lagarde, Franck Leroy, Marc, A Haffner, Philippe Petton, Bruno Cosseau, Celine Morga, Benjamin Dégremont, Lionel Mitta, Guillaume Grunau, Christoph Vidal-Dupiol, Jeremie |
author_facet |
Gawra, Janan Valdivieso, Alejandro Roux, Fabrice Laporte, Martin de Lorgeril, Julien Gueguen, Yannick Saccas, Mathilde Escoubas, Jean-Michel Montagnani, C. Destoumieux-Garzon, Delphine Lagarde, Franck Leroy, Marc, A Haffner, Philippe Petton, Bruno Cosseau, Celine Morga, Benjamin Dégremont, Lionel Mitta, Guillaume Grunau, Christoph Vidal-Dupiol, Jeremie |
author_sort |
Gawra, Janan |
title |
Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) |
title_short |
Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) |
title_full |
Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) |
title_fullStr |
Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) |
title_full_unstemmed |
Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) |
title_sort |
epigenetic then genetic variations underpin rapid adaptation of oyster populations (crassostrea gigas ) to pacific oyster mortality syndrome (poms) |
publisher |
HAL CCSD |
publishDate |
2024 |
url |
https://hal.science/hal-04651019 https://hal.science/hal-04651019/document https://hal.science/hal-04651019/file/Gawra-2023-BIORXIV.pdf https://doi.org/10.1101/2023.03.09.531494 |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
https://hal.science/hal-04651019 2024 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1101/2023.03.09.531494 hal-04651019 https://hal.science/hal-04651019 https://hal.science/hal-04651019/document https://hal.science/hal-04651019/file/Gawra-2023-BIORXIV.pdf BIORXIV: 2023.03.09.531494 doi:10.1101/2023.03.09.531494 |
op_rights |
http://creativecommons.org/licenses/by-nc-nd/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1101/2023.03.09.531494 |
_version_ |
1810440690692259840 |
spelling |
ftunivpolynesief:oai:HAL:hal-04651019v1 2024-09-15T18:03:10+00:00 Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas ) to Pacific Oyster Mortality Syndrome (POMS) Gawra, Janan Valdivieso, Alejandro Roux, Fabrice Laporte, Martin de Lorgeril, Julien Gueguen, Yannick Saccas, Mathilde Escoubas, Jean-Michel Montagnani, C. Destoumieux-Garzon, Delphine Lagarde, Franck Leroy, Marc, A Haffner, Philippe Petton, Bruno Cosseau, Celine Morga, Benjamin Dégremont, Lionel Mitta, Guillaume Grunau, Christoph Vidal-Dupiol, Jeremie Interactions Hôtes-Pathogènes-Environnements (IHPE) Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) Ministère de l'environnement Ministère de l'Environnement Laboratoire des Interactions Plantes Microbes Environnement (LIPME) Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE Nouvelle-Calédonie ) Institut de Recherche pour le Développement (IRD Nouvelle-Calédonie )-Délégation Ifremer de Nouvelle-Calédonie Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC)-Centre National de la Recherche Scientifique (CNRS) MARine Biodiversity Exploitation and Conservation - MARBEC (UMR MARBEC ) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Unité Adaptation et Santé des Invertébrés Marins (ASIM) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Ecosystèmes Insulaires Océaniens (UMR 241) (EIO) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé Papeete (ILM) Institut de Recherche pour le Développement (IRD) 2024-07-17 https://hal.science/hal-04651019 https://hal.science/hal-04651019/document https://hal.science/hal-04651019/file/Gawra-2023-BIORXIV.pdf https://doi.org/10.1101/2023.03.09.531494 en eng HAL CCSD info:eu-repo/semantics/altIdentifier/doi/10.1101/2023.03.09.531494 hal-04651019 https://hal.science/hal-04651019 https://hal.science/hal-04651019/document https://hal.science/hal-04651019/file/Gawra-2023-BIORXIV.pdf BIORXIV: 2023.03.09.531494 doi:10.1101/2023.03.09.531494 http://creativecommons.org/licenses/by-nc-nd/ info:eu-repo/semantics/OpenAccess https://hal.science/hal-04651019 2024 rapid adaptation genetic epigenetic POMS oyster exome capture [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity info:eu-repo/semantics/preprint Preprints, Working Papers, . 2024 ftunivpolynesief https://doi.org/10.1101/2023.03.09.531494 2024-07-22T14:02:32Z Disease emergence is accelerating in response to human activity-induced global changes. Understanding the mechanisms by which host populations can rapidly adapt to this threat will be crucial for developing future management practices. Pacific Oyster Mortality Syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations ( Crassostrea gigas) . Rapid adaptation to this disease may arise through both genetic and epigenetic mechanisms. In this study, we used a combination of whole exome capture of bisulfite-converted DNA, next-generation sequencing, and (epi)genome-wide association mapping, to show that natural oyster populations differentially exposed to POMS displayed signatures of selection both in their genome (single nucleotide polymorphisms) and epigenome (CG-context DNA methylation). Consistent with higher resistance to POMS, the genes targeted by genetic and epigenetic variations were mainly related to host immunity. By combining correlation analyses, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of the observed phenotypic variation was explained by interactions between the genetic sequence and epigenetic information, ∼14% by the genetic sequence, and up to 25% by the epigenome alone. Thus, as well as genetic adaptation, epigenetic mechanisms governing immune responses contribute significantly to the rapid adaptation of hosts to emerging infectious diseases. Report Crassostrea gigas Pacific oyster Université de la Polynésie française (upf): HAL |