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Pommier C, Michotey C, Cornut G, Roumet P, Duchêne E, Flores R, Lebreton A, Alaux M, Durand S, Kimmel E, Letellier T, Merceron G, Laine M, Guerche C, Loaec M, Steinbach D, Laporte MA, Arnaud E, Quesneville H, Adam-Blondon AF. Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS. Plant Phenomics 2019; 2019:1671403. [PMID: 33313522 PMCID: PMC7718628 DOI: 10.34133/2019/1671403] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/08/2019] [Indexed: 05/19/2023]
Abstract
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.
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Affiliation(s)
- C. Pommier
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - C. Michotey
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - G. Cornut
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - P. Roumet
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - E. Duchêne
- UMR SVQV, 28 rue de Herrlisheim, B.P. 20507, 68021 Colmar, France
| | - R. Flores
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - A. Lebreton
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - S. Durand
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - E. Kimmel
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - T. Letellier
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - G. Merceron
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. Laine
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - C. Guerche
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. Loaec
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - D. Steinbach
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - M. A. Laporte
- Bioversity International, parc Scientifique Agropolis II, 34397 Montpellier cedex 5, France
| | - E. Arnaud
- Bioversity International, parc Scientifique Agropolis II, 34397 Montpellier cedex 5, France
| | - H. Quesneville
- URGI, INRA, Université Paris-Saclay, 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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Paux E, Legeai F, Guilhot N, Adam-Blondon AF, Alaux M, Salse J, Sourdille P, Leroy P, Feuillet C. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics 2007. [PMID: 18038165 DOI: 10.1007/s10142‐007‐0068‐1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes.
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Affiliation(s)
- Etienne Paux
- INRA, UMR 1095, ASP, 234, avenue du Brézet, 63100, Clermont-Ferrand, France
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Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007; 449:463-7. [PMID: 17721507 DOI: 10.1038/nature06148] [Citation(s) in RCA: 2159] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 08/07/2007] [Indexed: 01/12/2023]
Abstract
The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
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Affiliation(s)
- Olivier Jaillon
- Genoscope (CEA) and UMR 8030 CNRS-Genoscope-Université d'Evry, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
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