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5 results on '"annotation fonctionnelle"'

1. Long noncoding RNA repertoire in chicken liver and adipose tissue

Author

Sylvain Foissac, Morgane Boutin, Valentin Wucher, Frédéric Jehl, Colette Désert, Elisabetta Giuffra, Diane Esquerre, Frédéric Lecerf, Sandrine Lagarrigue, Christophe Klopp, Kévin Muret, Thomas Derrien, Sarah Djebali, Fabrice Legeai, Hervé Acloque, BMC, BMC, Adapting the feed, the animal and the feeding techniques to improve the efficiency and sustainability of monogastric livestock production systems - Feed-a-Gene - - H20202015-03-01 - 2020-02-29 - 633531 - VALID, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, IN-1275570, INRA, European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, Genotype, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, poulet, génomique fonctionnelle, tissu adipeux, Adipose tissue, Biology, Genome, Evolution, Molecular, Transcriptome, Open Reading Frames, analyse de génome, 03 medical and health sciences, Genetics, Animals, Humans, RNA, Antisense, Genetics(clinical), RNA, Messenger, Gene, Conserved Sequence, Ecology, Evolution, Behavior and Systematics, Synteny, 030102 biochemistry & molecular biology, Gene Expression Profiling, General Medicine, Lipid Metabolism, foie, Phenotype, Long non-coding RNA, [SDV] Life Sciences [q-bio], Gene expression profiling, 030104 developmental biology, Adipose Tissue, Gene Expression Regulation, Liver, Organ Specificity, RNA, Long Noncoding, Animal Science and Zoology, Chickens, annotation fonctionnelle, Research Article
Abstract

Background Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling. Results We predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis. Conclusions We provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0275-0) contains supplementary material, which is available to authorized users.

Published
2017
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2. Profiling the landscape of transcription and chromatin conformation reveals regulatory mechanisms involved in immune and metabolic functions

Author

Sylvain Foissac, Sarah Djebali Quelen, Hervé Acloque, Marie-Helene Pinard - van der Laan, Sandrine Lagarrigue, Elisabetta Giuffra, ProdInra, Archive Ouverte, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), FAANG pilot project 'FR-AgENCODE', AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]

Subjects
pig, [SDV]Life Sciences [q-bio], chicken, génome, goat, animal de rente, T cells, functional annotation, liver, cash cattle, [SDV] Life Sciences [q-bio], cattle, chromatin, annotation fonctionnelle, chromatine
Abstract

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. Here we present on-going results on gene expression and chromatin conformation in hepatocytes and CD3+CD4+ (“CD4”) and CD3+CD8+ (“CD8”) T cells with a focus on the pig species (two male and two female Large White adult pigs). These samples were processed by strand-oriented RNA-seq and ATAC-seq experiments. Principal Component Analyses on log-transformed TMM-normalized read counts in genes (from RNA-seq) and regions of chromatin accessibility (from ATAC-seq) consistently highlighted the variability between liver and the T cells, and to a lesser extent within T cells (CD4 vs. CD8), as well as between the male and female samples. Comparative analyses identified differentially expressed genes between cell types as well as potential regulatory sites from differentially accessible chromatin regions. As expected, ontology annotations of differentially expressed genes were enriched for either immunity- or metabolism-related terms. Interestingly, correlations between gene expression and promoter accessibility across samples were enriched for both extreme positive and negative values, which suggests that ATAC-seq can efficiently capture distinct regulatory mechanisms of gene expression. Candidate enhancers and repressors were identified by comparing ATAC-seq regions with predicted binding sites of 500+ transcription factors. By integrating these results with those from Hi-C chromosome conformation capture on the liver samples, we investigated differences between “active” and “repressed” topological domains in terms of functional features, including gene density and general chromatin accessibility. Altogether, these results lead to a better understanding of the molecular mechanisms involved in pig immune and metabolic functions, and illustrate a useful contribution to the functional annotation effort of the FAANG initiative.

Published
2017

3. 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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4. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken

Author

Anis Djari, Diane Esquerre, Colette Désert, Sandrine Lagarrigue, Christophe Klopp, Morgane Boutin, Olivier Demeure, Pierre-François Roux, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), SIGENAE, Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Candidate gene, Heredity, Genetic Linkage, [SDV]Life Sciences [q-bio], génomique fonctionnelle, lcsh:Medicine, tissu adipeux, 0302 clinical medicine, INDEL Mutation, Genome Sequencing, lcsh:Science, Adiposity, Genetics, 0303 health sciences, Multidisciplinary, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Genome project, Genomics, Genetic Mapping, Linkage Analysis, annotation fonctionnelle, Research Article, cartographie de qtl, Genotype, Quantitative Trait Loci, poulet, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetic linkage, Animals, Obesity, Indel, Molecular Biology Techniques, Sequencing Techniques, Gene, Molecular Biology, Genetic Association Studies, 030304 developmental biology, Evolutionary Biology, Population Biology, High Throughput Sequencing, lcsh:R, Biology and Life Sciences, Computational Biology, Molecular Sequence Annotation, Genome Analysis, Genetic Polymorphism, lcsh:Q, Chickens, 030217 neurology & neurosurgery, Population Genetics
Abstract

In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.

Published
2014
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5. 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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