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4 results on '"annotation fonctionnelle"'

1. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Author

James W. Kijas, William S. Davidson, Steinar Bergseth, Patricia Iturra, Jon Olav Vik, Rachael J. Ritchie, Louis Bernatchez, Yniv Palti, Anna Wargelius, José M. Yáñez, Ross D. Houston, Craig R. Primmer, Matthew L. Rise, Kerry A. Naish, Alejandro Maass, Kristinn Olafsson, Tom Goldammer, Alfredo Tello, Patricia M. Schulte, Philip McGinnity, Martin Montecino, Sigbjørn Lien, Barbara F. Nowak, Krista M. Nichols, Ben F. Koop, Caird E. Rexroad, Yann Guiguen, Samuel A.M. Martin, Cristian Gallardo-Escárate, Stig W. Omholt, Graham Plastow, Simen Rød Sandve, Rodrigo Vidal, Daniel J. Macqueen, Institute of Biological and Environmental Sciences, (SFIRC), Department of Biology, Northern Arizona University [Flagstaff], The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval [Québec] (ULaval), The Research Council of Norway, Department of Molecular Biology and Biochemistry, University of California [Irvine] (UCI), University of California-University of California, Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, Universidad de Concepción [Chile], Institute for Genome Biology, Fish Genetics Unit, Leibniz Institute for Farm Animal Biology (FBN), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Human Genetics Program ICBM Faculty of Medicine, University of Chile, CSIRO, Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (NMBU), Center for Mathematical Modelling - Centro de Modelamiento Matematico [Santiago] (CMM), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), Center for Genome Regulation, FONDAP 15090007, School of Biological, Earth and Environmental Sciences [Sydney] (BEES), University of New South Wales [Sydney] (UNSW), Center for Biomedical Research, Universidad Andrés Bello [Santiago] (UNAB), FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, School of Aquatic and Fishery Sciences, University of Washington [Seattle], Conservation Biology Division [Seattle], Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), National Center for Cool and Cold Water Aquaculture, ARS-USDA, USDA-ARS : Agricultural Research Service, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Office of National Programs, Department of Ocean Sciences, Memorial University of Newfoundland [St. John's], Genome British Columbia, Department of Zoology, Auburn University (AU), INTESAL de SalmonChile, Instituto Tecnológico del Salmón S.A., Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Norwegian Institute of Marine Research, Faculty of Veterinary and Animal Sciences, Universidad de Chile = University of Chile [Santiago] (UCHILE), Aquainnovo, Supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8., University of Tasmania (UTAS), Université Laval, Universidad de Concepción, Leibniz Institute for Farm Animal Biology, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), University of Chile [Santiago]-Centre National de la Recherche Scientifique (CNRS), Matis Ltd, National Center for Cool and Cold Water Aquaculture, University of Chile [Santiago], and Supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada)), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8.

Subjects
0106 biological sciences, 0301 basic medicine, biologie comparative, Internationality, [SDV]Life Sciences [q-bio], Resistance, génomique fonctionnelle, Aquaculture, 01 natural sciences, Genome, genomic selection, Whole genome duplication, poisson, salmonids, Applied research, évolution génomique des poissons, duplication des génomes, Phylogeny, Genetics, DNA methylation, Populations, Functional annotation, Genomics, Salar, ChIP-seq, phénotype, Rainbow trout, Molecular Sequence Annotation, séquençage du génome, Editorial, Phenotype, Phenotyping, aquaculture, comparative biology, data sharing, evolution, functional annotation, genome biology, phenotyping, standardized data and metadata, salmonid fish, whole genome duplication, Identification (biology), annotation fonctionnelle, Salmonidae, Biotechnology, expression des gènes, Atlantic salmon, Genome evolution, Conservation of Natural Resources, lcsh:QH426-470, Evolution, lcsh:Biotechnology, Comparative biology, Biology, Insights, 010603 evolutionary biology, production aquacole, reproduction, Evolution, Molecular, 03 medical and health sciences, analyse de génome, Standardized data and metadata, lcsh:TP248.13-248.65, Animals, 14. Life underwater, sélection génomique, conservation des espèces, fish, Oncorhynchus tshawytscha, lcsh:Genetics, 030104 developmental biology, Genome biology, Evolutionary biology, variation phénotypique, Genome Biology, Standardized data and, Data sharing, évolution génomique, Salmonid fish
Abstract

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)

Published
2017
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2. Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Author

Macqueen, Daniel J., Primmer, Craig R., Houston, Ross D., Nowak, Barbara F., Bernatchez, Louis, Bergseth, Steinar, Davidson, William S., Gallardo-Escárate, Cristian, Goldammer, Tom, Guiguen, Yann, Iturra, Patricia, Kijas, James W., Koop, Ben F., Lien, Sigbjørn, Maass, Alejandro, Martin, Samuel A.M., McGinnity, Philip, Montecino, Martin, Naish, Kerry A., Nichols, Krista M., Ólafsson, Kristinn, Omholt, Stig W., Palti, Yniv, Plastow, Graham S., Rexroad, Caird E., Rise, Matthew L., Ritchie, Rachael J., Sandve, Simen R., Schulte, Patricia M., Tello, Alfredo, Vidal, Rodrigo, Vik, Jon O., Wargelius, Anna, and Yáñez, José Manuel

Subjects
salmonidae, biologie comparative, génomique fonctionnelle, production aquacole, reproduction, analyse de génome, phénotype, séquençage du génome, poisson, aquaculture, variation phénotypique, comparative biology, data sharing, evolution, functional annotation, genome biology, phenotyping, standardized data and metadata, salmonid fish, whole genome duplication, évolution génomique des poissons, sélection génomique, évolution génomique, annotation fonctionnelle, conservation des espèces, duplication des génomes, expression des gènes
Abstract

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Published
2016

3. dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

Author

Pierre Martre, Jonathan Vincent, Zhanwu Dai, M. Fouad Bouzidi, Marie Agier, Frédéric Choulet, Catherine Ravel, Said Mouzeyar, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure des Mines de St Etienne, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut des Sciences de la Vigne et du Vin (ISVV)-Université de Bordeaux (UB), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)-Université Victor Segalen - Bordeaux 2-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Arabidopsis, UniGene, Computational biology, Biology, Genes, Plant, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, Homology (biology), 03 medical and health sciences, Annotation, Gene Expression Regulation, Plant, Databases, Genetic, Gene family, triticum aestivum, RNA, Messenger, analyse du transcriptome, Gene, Triticum, 030304 developmental biology, 2. Zero hunger, Genetics, base de données, 0303 health sciences, Expressed sequence tag, Internet, Alkyl and Aryl Transferases, Gene Expression Profiling, arabidopsis thaliana, food and beverages, Gene Expression Regulation, Developmental, Molecular Sequence Annotation, Oryza, oryza sativa, Database Tool, Geranylgeranyl-Diphosphate Geranylgeranyltransferase, Proteome, Seeds, General Agricultural and Biological Sciences, annotation fonctionnelle, Glycolysis, 010606 plant biology & botany, Information Systems, expression des gènes
Abstract

The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL: urgi.versailles.inra.fr/dbWFA/

Published
2013
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4. Populus Genome Portal

Author

Bourgait, Isabelle, Ghazali, Farid, Koyao-Darinest, Vivianne Judith, Jorge, Véronique, Samson, Franck, Aubourg, Sebastien, Pilate, Gilles, Label, Philippe, Leplé, Jean-Charles, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
méthode sage, GENE EXPRESSION, EXPRESSED SEQUENCE TAG, carte génétique, STRUCTURE DU GENOME, BIOINFORMATIC CLUSTERING, QTL, génome, [SDV]Life Sciences [q-bio], MICROARRAY, GENETIC MAP, SAGE, ANNOTATION, PEUPLIER, assemblage bioinformatique, populus, étiquette de séquence transcrite, puce à adn, annotation fonctionnelle, bioinformatique, expression des gènes
Abstract

Événement(s) lié(s) : - IUFRO Tree Biotechnology Conference; Whistler (CAN) - (2009-06-28 - 2009-07-02); International audience; The Poplar Genome Portal project will provide a virtual meeting place for the research community interested in poplar genomics through web access to curated and interoperable relational databases. This project is complementary to the Dendrome project, mainly focused on conifer genomes. Present databases gather gene expression data (EST, SAGE, microarrays), functional annotation, genetic maps, QTLs, SNP and phenotypic data. The expression-database holds 328,583 quality-filtered ESTs representing 96 cDNA libraries. New tools enable SAGE tags analysis and electronic northern statistics coupled with poplar genome annotation. Among 371,226 worldwide public sequences, 89% were quality-filtered mainly through vector curation, nucleotide-duplication error detection and minimum sequence length. 94% of filtered EST were aligned on poplar Genome using FLAGdb++ tools. Part of this work is presently accessible through FLAGdb++ environment, a friendly-user graphical interface ((http://urgv.evry.inra.fr/FLAGdb). We developed web tools to cross-analyze various types of data, i.e. genetic map, gene models, Affymetrix probeset annotation and gene expression data.

Published
2009

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