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2 results on '"FR-AgENCODE"'

1. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, der Laan, Marie-Hélène Pinard-Van, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, Giuffra, Elisabetta, 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 de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), 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), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 ), Université de Rennes (UR), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris Saclay (COMUE), INRA 'SelGen metaprogramme', grant 'FR-AgENCODE: A French pilot project to enrich the annotation of livestock genomes' (2015-2017), Animal Health and Welfare ERA-Net (anihwa) -project KILLeuPRRSV, ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), European Project: FP7-609398, 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], Curtin University, GeT PlaGe, Genotoul, 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 ), Université de Rennes (UNIV-RENNES), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), CEA Paris Saclay, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), 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, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Institut National de la Recherche Agronomique (INRA), 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 des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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 Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
Livestock, Goats, [SDV]Life Sciences [q-bio], Sus scrofa, Molecular Sequence Annotation, Functional annotation, ATAC-seq, Chromatin, lcsh:Biology (General), Hi-C, Animals, Domestic, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Animals, Cattle, RNA-seq, Transcriptome, Chickens, lcsh:QH301-705.5, Phylogeny, Research Article
Abstract

Background Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. Conclusions We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Published
2019
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2. GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

Author

Tuggle, Christopher, Giuffra, Elisabetta, White, Stephen, Clarke, Laura, Zhou, Huaijun, Ross, Pablo, Finno, Carrie, Acloque, H., Reecy, James, Archibald, Alan, Bellone ¶ ¶, Rebecca, Boichard, Michèle, Chamberlain, Amanda, Cheng, Hans, Crooijmans, Richard, Delany, Mary, Finno, Carrie J., Groenen, Martien, Hayes, Ben, Lunney, Joan, Petersen, Jessica, Plastow, Graham, Schmidt, Carl, Song, Jiuzhou, Watson, Mick, Iowa State University (ISU), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, USDA-ARS : Agricultural Research Service, Center for Reproductive Biology, Washington State University (WSU), Department of Veterinary Microbiology and Pathology, European Molecular Biology Laboratory, European Bioinformatics Institute, Department of Animal Science, University of California, Department of Population Health and Reproduction, 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, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Department of Population Health and Reproduction, School of Veterinary Medicine, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Avian Disease and Oncology Laboratory, 4279 E Mount Hope Road, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Centre for Nutrition and Food Sciences - Queensland Alliance for Agriculture and Food Innovation, University of Southern Queensland (USQ), Animal Parasitic Diseases Laboratory [Beltsville, USA], United States Department of Agriculture (USDA)-USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Department of Agricultural, Food & Nutritional Science, University of Alberta, Department of Animal & Food Sciences, University of Delaware [Newark], Department of Animal and Avian Sciences, University of Maryland [College Park], University of Maryland System-University of Maryland System, National Science Foundation (NSF) NSF-IOS-1548275, United States Department of Agriculture (USDA) USDA-NIFA-AFRI, 2015-68004-24104, Illumina, Inc, Iowa State University, USDA-NRSP-8 Bioinformatics, United States Department of Agriculture (USDA) 2016-67015-24579, Genome Canada, Affymetrix, Inc, Geneseek, Inc, Biotechnology and Biological Sciences Research Council including Institute Strategic Programme and National Capability Grants (BBSRC) BBS/E/D/20310000 BB/J004243/1, INRA through the SelGen metaprogramme (Fr-AgENCODE project), Biotechnology and Biological Sciences Research Council (BBSRC) : BBS/E/D/20211551, BBS/E/D/20211550, BBS/E/D/20310000, BB/M01844X/1., United States Department of Agriculture (USDA), European Molecular Biology Laboratory European Bioinformatics Institute, University of California [Davis] (UC Davis), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT], Roslin Institute, Wageningen University and Research Centre (WUR), University of Queensland [Brisbane], Dept Anim & Food Sci, and University of Maryland System

Subjects
data coordination centre (DCC), Dairy & Animal Science, [SDV]Life Sciences [q-bio], International Cooperation, data sharing, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, dna, Animal Breeding and Genomics, metanalysis, genomic, Genetics, Animals, [INFO]Computer Science [cs], Fokkerij en Genomica, Veterinary Sciences, Domestic, [SDV.GEN]Life Sciences [q-bio]/Genetics, regulatory variation, Genome, Genomics, Articles, Congresses as Topic, Reference Standards, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, reveal principle, data coordination centre, Animals, Domestic, District of Columbia, WIAS, chromatin, Original Article, Zoology
Abstract

International audience; The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7-8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Published
2016
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