Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution
International audience The generation of EST information is an essential step in the genomic characterisation of species. In the context of the European Network Marine Genomics, a common goal was to significantly increase the amount of ESTs in commercial marine mollusk species and more specifically...
Published in: | Gene |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2008
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Subjects: | |
Online Access: | https://hal.archives-ouvertes.fr/halsde-00450595 https://doi.org/10.1016/j.gene.2007.10.021 |
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ftccsdartic:oai:HAL:halsde-00450595v1 |
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Open Polar |
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Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
Molluscs ESTs Environment Evolution [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp |
spellingShingle |
Molluscs ESTs Environment Evolution [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp Tanguy, Arnaud Bierne, Nicolas Saavedra, Carlos Pina, Benjamin Bachère, Evelyne Kube, Michael Bazin, Eric Bonhomme, François Boudry, Pierre Boulo, Viviane Boutet, Isabelle Cancela, Leonor, Dossat, Carole Favrel, Pascal Huvet, Arnaud Jarque, Sergio Jollivet, Didier Klages, Sven Lapegue, Sylvie Leite, Ricardo Moal, Jeanne Moraga, Dario Reinhardt, Richard Samain, Jean-François Zouros, Eleftherios Canario, Adelino Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution |
topic_facet |
Molluscs ESTs Environment Evolution [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp |
description |
International audience The generation of EST information is an essential step in the genomic characterisation of species. In the context of the European Network Marine Genomics, a common goal was to significantly increase the amount of ESTs in commercial marine mollusk species and more specifically in the less studied but ecologically and commercially important groups, such as mussel and clam genera. Normalized cDNA libraries were constructed for four different relevant bivalves species (Crassostrea gigas, Mytilus edulis, Ruditapes decussatus and Bathymodiolus azoricus), using numerous tissues and physiological conditions. In this paper, we present the analysis of the 13,013 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1300–3000 unique sequences were identified in each species. For the different species, functional categories could be assigned to only about 16 to 27% of ESTs using the GO annotation tool. All sequences have been incorporated into a publicly available database and form the basis for subsequent microarray design, SNP detection and polymorphism analysis, and the placement of novel markers on genetic linkage maps. |
author2 |
Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Instituto de Acuicultura de Torre la Sal (IATS) Consejo Superior de Investigaciones Científicas Madrid (CSIC) IBMB-CSIC Génome, populations, interactions, adaptation (GPIA) Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2) Max Planck Institute for Molecular Genetics (MPIMG) Max-Planck-Gesellschaft Laboratoire de Génétique et Pathologie (LGP) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Centre of Marine Sciences Faro (CCMAR) University of Algarve Portugal Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Physiologie et Ecophysiologie des Mollusques Marins (PE2M) Université de Caen Normandie (UNICAEN) Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS) Adaptation et diversité en milieu marin (AD2M) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO) Department of Biology University of Crete Heraklion (UOC) Centro de Ciências do Mar Faro (CCMAR) Universidade do Algarve (UAlg) |
format |
Article in Journal/Newspaper |
author |
Tanguy, Arnaud Bierne, Nicolas Saavedra, Carlos Pina, Benjamin Bachère, Evelyne Kube, Michael Bazin, Eric Bonhomme, François Boudry, Pierre Boulo, Viviane Boutet, Isabelle Cancela, Leonor, Dossat, Carole Favrel, Pascal Huvet, Arnaud Jarque, Sergio Jollivet, Didier Klages, Sven Lapegue, Sylvie Leite, Ricardo Moal, Jeanne Moraga, Dario Reinhardt, Richard Samain, Jean-François Zouros, Eleftherios Canario, Adelino |
author_facet |
Tanguy, Arnaud Bierne, Nicolas Saavedra, Carlos Pina, Benjamin Bachère, Evelyne Kube, Michael Bazin, Eric Bonhomme, François Boudry, Pierre Boulo, Viviane Boutet, Isabelle Cancela, Leonor, Dossat, Carole Favrel, Pascal Huvet, Arnaud Jarque, Sergio Jollivet, Didier Klages, Sven Lapegue, Sylvie Leite, Ricardo Moal, Jeanne Moraga, Dario Reinhardt, Richard Samain, Jean-François Zouros, Eleftherios Canario, Adelino |
author_sort |
Tanguy, Arnaud |
title |
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution |
title_short |
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution |
title_full |
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution |
title_fullStr |
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution |
title_full_unstemmed |
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution |
title_sort |
increasing genomic information in bivalves through new est collections in four species: development of new genetic markers for environmental studies and genome evolution |
publisher |
HAL CCSD |
publishDate |
2008 |
url |
https://hal.archives-ouvertes.fr/halsde-00450595 https://doi.org/10.1016/j.gene.2007.10.021 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
ISSN: 0378-1119 EISSN: 1879-0038 Gene https://hal.archives-ouvertes.fr/halsde-00450595 Gene, Elsevier, 2008, 408 (1-2), pp.27-36. ⟨10.1016/j.gene.2007.10.021⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.gene.2007.10.021 halsde-00450595 https://hal.archives-ouvertes.fr/halsde-00450595 doi:10.1016/j.gene.2007.10.021 |
op_doi |
https://doi.org/10.1016/j.gene.2007.10.021 |
container_title |
Gene |
container_volume |
408 |
container_issue |
1-2 |
container_start_page |
27 |
op_container_end_page |
36 |
_version_ |
1766394441696804864 |
spelling |
ftccsdartic:oai:HAL:halsde-00450595v1 2023-05-15T15:58:40+02:00 Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution Tanguy, Arnaud Bierne, Nicolas Saavedra, Carlos Pina, Benjamin Bachère, Evelyne Kube, Michael Bazin, Eric Bonhomme, François Boudry, Pierre Boulo, Viviane Boutet, Isabelle Cancela, Leonor, Dossat, Carole Favrel, Pascal Huvet, Arnaud Jarque, Sergio Jollivet, Didier Klages, Sven Lapegue, Sylvie Leite, Ricardo Moal, Jeanne Moraga, Dario Reinhardt, Richard Samain, Jean-François Zouros, Eleftherios Canario, Adelino Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Instituto de Acuicultura de Torre la Sal (IATS) Consejo Superior de Investigaciones Científicas Madrid (CSIC) IBMB-CSIC Génome, populations, interactions, adaptation (GPIA) Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2) Max Planck Institute for Molecular Genetics (MPIMG) Max-Planck-Gesellschaft Laboratoire de Génétique et Pathologie (LGP) Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) Centre of Marine Sciences Faro (CCMAR) University of Algarve Portugal Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) Physiologie et Ecophysiologie des Mollusques Marins (PE2M) Université de Caen Normandie (UNICAEN) Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS) Adaptation et diversité en milieu marin (AD2M) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO) Department of Biology University of Crete Heraklion (UOC) Centro de Ciências do Mar Faro (CCMAR) Universidade do Algarve (UAlg) 2008-01 https://hal.archives-ouvertes.fr/halsde-00450595 https://doi.org/10.1016/j.gene.2007.10.021 en eng HAL CCSD Elsevier info:eu-repo/semantics/altIdentifier/doi/10.1016/j.gene.2007.10.021 halsde-00450595 https://hal.archives-ouvertes.fr/halsde-00450595 doi:10.1016/j.gene.2007.10.021 ISSN: 0378-1119 EISSN: 1879-0038 Gene https://hal.archives-ouvertes.fr/halsde-00450595 Gene, Elsevier, 2008, 408 (1-2), pp.27-36. ⟨10.1016/j.gene.2007.10.021⟩ Molluscs ESTs Environment Evolution [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp info:eu-repo/semantics/article Journal articles 2008 ftccsdartic https://doi.org/10.1016/j.gene.2007.10.021 2021-12-19T03:56:18Z International audience The generation of EST information is an essential step in the genomic characterisation of species. In the context of the European Network Marine Genomics, a common goal was to significantly increase the amount of ESTs in commercial marine mollusk species and more specifically in the less studied but ecologically and commercially important groups, such as mussel and clam genera. Normalized cDNA libraries were constructed for four different relevant bivalves species (Crassostrea gigas, Mytilus edulis, Ruditapes decussatus and Bathymodiolus azoricus), using numerous tissues and physiological conditions. In this paper, we present the analysis of the 13,013 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1300–3000 unique sequences were identified in each species. For the different species, functional categories could be assigned to only about 16 to 27% of ESTs using the GO annotation tool. All sequences have been incorporated into a publicly available database and form the basis for subsequent microarray design, SNP detection and polymorphism analysis, and the placement of novel markers on genetic linkage maps. Article in Journal/Newspaper Crassostrea gigas Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Gene 408 1-2 27 36 |