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Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchêne E, Choisne N, Mohellibi N, Guichard C, Rombauts S, Le Clainche I, Bérard A, Chauveau A, Bounon R, Rustenholz C, Morgante M, Le Paslier MC, Brunel D, Adam-Blondon AF. A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genom Data 2017; 14:56-62. [PMID: 28971018 PMCID: PMC5612791 DOI: 10.1016/j.gdata.2017.09.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 11/21/2022]
Affiliation(s)
- A Canaguier
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - J Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño 26007, Spain
| | | | | | - E Duchêne
- SVQV, UMR 1131, INRA, Université de Strasbourg, 28 rue de Herrlisheim, 68000 Colmar, France
| | - N Choisne
- URGI, UR 1164, INRA, Université Paris-Saclay, route de Saint-Cyr, 78026 Versailles, France
| | - N Mohellibi
- URGI, UR 1164, INRA, Université Paris-Saclay, route de Saint-Cyr, 78026 Versailles, France
| | - C Guichard
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,IPS2, UMR 1403, INRA, Université Paris-Saclay, Rue de Noetzlin, bât. 630, 91190 Gif-sur-Yvette, France
| | - S Rombauts
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
| | - I Le Clainche
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - A Bérard
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - A Chauveau
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - R Bounon
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - C Rustenholz
- SVQV, UMR 1131, INRA, Université de Strasbourg, 28 rue de Herrlisheim, 68000 Colmar, France
| | - M Morgante
- IGA, via J. Linussio 51, 33100 Udine, Italy
| | - M-C Le Paslier
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - D Brunel
- EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France
| | - A-F Adam-Blondon
- UMR GV, INRA, UEVE, ERL CNRS, 2 rue Gaston Crémieux, 91000 Evry, France.,URGI, UR 1164, INRA, Université Paris-Saclay, route de Saint-Cyr, 78026 Versailles, France
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Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H. Towards an open grapevine information system. Hortic Res 2016; 3:16056. [PMID: 27917288 PMCID: PMC5120350 DOI: 10.1038/hortres.2016.56] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/10/2016] [Accepted: 10/21/2016] [Indexed: 05/26/2023]
Abstract
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.
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Affiliation(s)
- A-F Adam-Blondon
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - M Alaux
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - C Pommier
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
| | - D Cantu
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Z-M Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - GR Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - C Davies
- CSIRO Agriculture and Food, Waite Campus, WIC West Building, PMB2, Glen Osmond, South Australia 5064, Australia
| | - S Delrot
- Université de Bordeaux, ISVV, EGFV, UMR 1287, F-33140 Villenave d’Ornon, France
| | - L Deluc
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - G Di Gaspero
- Istituto di Genomica Applicata, Udine 33100, Italy
| | - J Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño 26006, Spain
| | - A Fennell
- Plant Science Department, South Dakota State University, BioSNTR, Brookings, SD 57007, USA
| | - JP Londo
- United States Department of Agriculture-Agricultural Research Service-Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - P Kersey
- European Molecular Biology Laboratory, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - F Mattivi
- Dipartimento Qualità Alimentare e Nutrizione, Centro Ricerca ed Innovazione Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italia
| | - S Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - P Neveu
- UMR Mistea, INRA, Montpellier 34060, France
| | - M Nikolski
- University of Bordeaux, CBiB, Bordeaux 33000, France
- University of Bordeaux, CNRS/LaBRI, Talence 33405, France
| | - M Pezzotti
- Department of Biotechnology, Università degli Studi di Verona, Verona 37134, Italy
| | - BI Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - R Töpfer
- JKI Institute for Grapevine Breeding Geilweilerhof, Siebeldingen 76833, Germany
| | - MA Vivier
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, Matieland 7602, South Africa
| | - D Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- US Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - H Quesneville
- URGI, UR1164 INRA, Université Paris-Saclay, Versailles 78026, France
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