26 results on '"Hueber, Yann"'
Search Results
2. Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee
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Lashermes, Philippe, Combes, Marie-Christine, Hueber, Yann, Severac, Dany, and Dereeper, Alexis
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- 2014
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Catalog
3. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas
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Cenci, Alberto, Sardos, Julie, Hueber, Yann, Martin, Guillaume, Breton, Catherine, Roux, Nicolas, Swennen, Rony, Carpentier, Sébastien Christian, Rouard, Mathieu, Cenci, Alberto, Sardos, Julie, Hueber, Yann, Martin, Guillaume, Breton, Catherine, Roux, Nicolas, Swennen, Rony, Carpentier, Sébastien Christian, and Rouard, Mathieu more...
- Abstract
Background and Aims: Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. Methods: Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. Key Results: Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. Conclusions: The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic more...
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- 2021
4. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas
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Cenci, Alberto, primary, Sardos, Julie, additional, Hueber, Yann, additional, Martin, Guillaume, additional, Breton, Catherine, additional, Roux, Nicolas, additional, Swennen, Rony, additional, Carpentier, Sebastien Christian, additional, and Rouard, Mathieu, additional more...
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- 2020
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5. Unraveling the complex story of intergenomic recombination in ABB allotriploid bananas
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Martin Guillaume, Cenci Alberto, Sardos Julie, Breton Catherine, Carpentier Sebastien Christian, Roux Nicolas, Hueber Yann, Rouard Mathieu, and Swennen Rony
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Polyploid ,Snp markers ,Evolutionary biology ,Chromosome ,food and beverages ,Cultivar ,Biology ,Parthenocarpy ,Genome ,Recombination ,Hybrid - Abstract
Background and AimsBananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB, or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security.MethodsUsing SNP markers called from RAD-Seq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we search for similar events within nine AB hybrid genotypes.Key ResultsRecurrent Homoeologous Exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes were unraveled with at least 9 founding events at the origin of the ABB bananas prior to the clonal diversification. The discovery of this nine founding events allows discussing the possible routes that led to the creation of the different subgroups and formulate new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars. Routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploid originated and where cultivated M. balbisiana are abundant.ConclusionsThe result of this study clarifies the classification of ABB cultivars and leading possibly to the revision of the classification of this subgroup. This is an important step to unravel the origin of polyploid bananas, and contributes to possible scenarios on the origin. ABB bananas are hypothesized to be more drought tolerant. Knowing the origin of our current cultivars and so their potential parents will help breeders to make the right choices for future crosses. The M. balbisiana genome is a good source to create new cultivars able to answer the numerous challenges of banana breeding. more...
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- 2019
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6. Gigwa v2—Extended and improved genotype investigator
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Sempéré, Guilhem, Pétel, Adrien, Rouard, Mathieu, Frouin, Julien, Hueber, Yann, De Bellis, Fabien, Larmande, Pierre, Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Institut National de la Recherche Agronomique (INRA), Université de Montpellier (UM), CGIAR, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), French National Research Agency (ANR) : ANR-16-IDEX-0006, and ANR-16-IDEX-0006,MUSE,MUSE(2016) more...
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Genotype ,SNP ,interoperability ,Logiciel ,Polymorphism, Single Nucleotide ,web ,F30 - Génétique et amélioration des plantes ,génomique ,HapMap ,User-Computer Interface ,Variation génétique ,MongoDB ,Databases, Genetic ,Technical Note ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,PLINK ,Humans ,Traitement des données ,Internet ,Vegetal Biology ,genomic variations ,VCF ,NoSQL ,indel ,REST ,BrAPI ,GA4GH ,Computational Biology ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Genomics ,L10 - Génétique et amélioration des animaux ,interopérabilité ,U30 - Méthodes de recherche ,Biologie végétale ,Génotype ,Software - Abstract
International audience; Background: The study of genetic variations is the basis of many research domains in biology. From genome structure to population dynamics, many applications involve the use of genetic variants. The advent of next-generation sequencing technologies led to such a flood of data that the daily work of scientists is often more focused on data management than data analysis. This mass of genotyping data poses several computational challenges in terms of storage, search, sharing, analysis, and visualization. While existing tools try to solve these challenges, few of them offer a comprehensive and scalable solution. Results: Gigwa v2 is an easy-to-use, species-agnostic web application for managing and exploring high-density genotyping data. It can handle multiple databases and may be installed on a local computer or deployed as an online data portal. It supports various standard import and export formats, provides advanced filtering options, and offers means to visualize density charts or push selected data into various stand-alone or online tools. It implements 2 standard RESTful application programming interfaces, GA4GH, which is health-oriented, and BrAPI, which is breeding-oriented, thus offering wide possibilities of interaction with third-party applications. The project home page provides a list of live instances allowing users to test the system on public data (or reasonably sized user-provided data). Conclusions: This new version of Gigwa provides a more intuitive and more powerful way to explore large amounts of genotyping data by offering a scalable solution to search for genotype patterns, functional annotations, or more complex filtering. Furthermore, its user-friendliness and interoperability make it widely accessible to the life science community. more...
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- 2019
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7. Managing and exploring large genotyping data with Gigwa
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Sempere, Guilhem, Petel, Adrien, Rouard, Mathieu, Larmande, Pierre, Hueber, Yann, Frouin, Julien, and De Bellis, Fabien
- Abstract
With the decreasing cost of genome sequencing, many laboratories are increasingly adopting genotyping technologies as a routine component of their analytical workflows, generating large datasets (e.g. VCF files) of genotyping information. Nevertheless, manipulating such large datasets remains a challenge for many scientists. In this context, we developed Gigwa (Genotype Investigator for Genome-Wide Analyses) with the aim of providing a user-friendly system to meet the requirements of scientists who need to filter large datasets and export them into various formats for subsequent analyses. Gigwa is species-agnostic, cross-platform, scalable and easy to deploy. It can be configured to run on a local computer or setup across servers to act as a data portal. It may be used to share data with collaborators while providing means to seek variants of interest based on location, functional annotations or genotype patterns. Based on NoSQL technology, it supports very large datasets (up to tens of millions of genotypes) when configured on suitable hardware. Its most attractive features are: ergonomic interface including user management, numerous import and export formats, powerful filtering engine, interoperability via REST APIs and connection to online or standalone tools. Gigwa now in version 2 (http://gigwa.southgreen.fr), is developed within the scope of South Green bioinformatics, a cross-institute platform and community dedicated to genetics and genomics of tropical and Mediterranean plants, based in Montpellier, France. more...
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- 2019
8. Additional file 5: of Effect of paleopolyploidy and allopolyploidy on gene expression in banana
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Cenci, Alberto, Hueber, Yann, Zorrilla-Fontanesi, Yasmin, Wesemael, Jelle, Ewaut Kissel, Gislard, Marie, Sardos, Julie, Swennen, Rony, Roux, Nicolas, Carpentier, Sebastien, and Rouard, Mathieu
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Sample of genes differentially expressed in ‘Cachaco’ (ABB) compared to AAA cultivars (‘Mbwazirume’ and ‘Grande Naine’). (DOCX 18 kb)
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- 2019
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9. Additional file 2: of Effect of paleopolyploidy and allopolyploidy on gene expression in banana
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Cenci, Alberto, Hueber, Yann, Zorrilla-Fontanesi, Yasmin, Wesemael, Jelle, Ewaut Kissel, Gislard, Marie, Sardos, Julie, Swennen, Rony, Roux, Nicolas, Carpentier, Sebastien, and Rouard, Mathieu
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Chromosome intervals (defined on genes coordinates) showing B:A ratio deviating from the expected genomic constitution. CDM indicates the three cultivars sharing the same pattern of deviating regions (‘Cachaco’, ‘Dole’ and ‘Monthan’). (DOCX 16 kb) more...
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- 2019
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10. Additional file 6: of Effect of paleopolyploidy and allopolyploidy on gene expression in banana
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Cenci, Alberto, Hueber, Yann, Zorrilla-Fontanesi, Yasmin, Wesemael, Jelle, Ewaut Kissel, Gislard, Marie, Sardos, Julie, Swennen, Rony, Roux, Nicolas, Carpentier, Sebastien, and Rouard, Mathieu
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Histograms representing the paralog included expression (normalized read count, Y axis) for 58 genes having significant higher expression in ‘Cachaco’ (Ca) than in ‘Grande Naine’ (GN) and ‘Mbwazirume’ (Mb). Blue color represents expression level of DEG, other colors expression level of respective paralogs. (PPTX 146 kb) more...
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- 2019
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11. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)
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Rouard, Mathieu, Droc, Gaëtan, Martin, Guillaume, Sardos, Julie, Hueber, Yann, Guignon, Valentin, Cenci, Alberto, Geigle, B., Hibbins, M.S., Yahiaoui, Nabila, Baurens, Franc-Christophe, Berry, Vinvent, Hahn, M.W., D'Hont, Angélique, Roux, Nicolas, Rouard, Mathieu, Droc, Gaëtan, Martin, Guillaume, Sardos, Julie, Hueber, Yann, Guignon, Valentin, Cenci, Alberto, Geigle, B., Hibbins, M.S., Yahiaoui, Nabila, Baurens, Franc-Christophe, Berry, Vinvent, Hahn, M.W., D'Hont, Angélique, and Roux, Nicolas more...
- Abstract
Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees. more...
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- 2018
12. The South Green Bioinformatics platform, a comprehensive resource for crop genomics
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Manuel Ruiz, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Tranchant-Dubreuil, Christine, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, Lamotte, Frédéric, Larmande, Pierre, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, This, Dominique, stéphanie bocs, Hueber, Yann, El Hassouni, Nordine, Guillaume Martin, Gkanogiannis, Anestis, Sébastien RAVEL, Monat, Cécile, Tando, Ndomassi, and Rouard, Mathieu more...
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ComputingMethodologies_PATTERNRECOGNITION ,food and beverages - Abstract
Analysis and visualization of massive genomics datasets are an ongoing trend in plant sciences. The South Green Bioinformatics platform provides an ecosystem of tools that were originally developed as independent entities to fulfill the need for specific projects or crops, but have evolved over time to generic tools to comprehensively study crop genomics. We have built a large panel of public information systems dedicated to specialized datasets (markers, genes, gene families, transcriptomes, genotypes, phenotypes, etc.) and crop-specific resources called Genome Hubs. Target users of bioinformatic analytical workflows are usually divided between people who use command-line and those who do not. We addressed both categories by offering complementary solutions, like Galaxy-based and command-line applications. Various groups used the South Green infrastructure to obtain their data and results, and were able to publish high-quality biological information, on Coffee genome, Banana, Cocoa, African rice or large transcriptome resources. Tools developed for these studies are adaptable to a wide range of other organisms. more...
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- 2017
13. South Green bioinformatics platform : Plateforme collaborative de bioinformatique verte héraultaise
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Bocs, Stéphanie, Couvin, David, De Lamotte, Frédéric, Dereeper, Alexis, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Gkanogiannis, Anestis, Guignon, Valentin, Hamelin, Chantal, Hueber, Yann, Larivière, Delphine, Larmande, Pierre, Martin, Guillaume, Monat, Cécile, Ortega Abboud, Enrique, Pitollat, Bertrand, Pointet, Stéphanie, Ravel, Sébastien, Rouard, Mathieu, This, Patrice, and Tranchant-Dubreuil, Christine more...
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- 2017
14. Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
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van Wesemael, Jelle, primary, Hueber, Yann, additional, Kissel, Ewaut, additional, Campos, Nádia, additional, Swennen, Rony, additional, and Carpentier, Sebastien, additional
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- 2018
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15. One hundred and six diploids to unravel the genetics of traits in banana: a panel for genome-wide association study and its application to the seedless phenotype. [W075]
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Sardos, Julie, Rouard, Mathieu, Hueber, Yann, Cenci, Alberto, Hyma, Katie E., Van Den Houwe, Ines, Hribova, Eva, Courtois, Brigitte, and Roux, Nicolas
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F60 - Physiologie et biochimie végétales ,fungi ,food and beverages ,U30 - Méthodes de recherche ,F30 - Génétique et amélioration des plantes - Abstract
Banana is a fruit crop with a complex diversity pattern resulting from a complex domestication scheme. Due to the availability of plant genome sequences and to the accessibility of next-generation genotyping technologies, Genome-Wide Association Studies (GWAS) have been increasingly performed in crop plants as a start to resolve genetic architecture of traits. The GWAS method was developed to perform association studies between phenotypes such as diseases and genotypes in Humans and is now successfully applied to many plants and animals to support the breeding process. However, there are prerequisites for such methods as it has been designed for populations of diploids organisms which follow the mendelian genetics model (i.e. “infinite” population and panmixia). In banana, the most popular cultivars are triploids, often hybrids between different species, and due to the absence of seeds in the fruit, a wide amount of the diversity observed ensues from the clonal diversification of a few initial genotypes. Therefore, the application of such approach to the crop is challenging and innovative. We selected a set of 106 diploid accessions with pure M. acuminata background avoiding clone duplicates and generated the appropriate molecular markers to support GWAS for any given trait. Finally, we validated the approach on the major domestication syndrome in banana, the seedless phenotype, and identified six candidate regions in which are located two strong candidate genes for female sterility. (Texte intégral) more...
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- 2016
16. South Green bioinformatics platform: Update 2015
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Armero, A., Baurens, Franc-Christophe, stéphanie bocs, Breil, A., Lamotte, Frédéric, Dereeper, Alexis, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Olivier Garsmeur, Guignon, Valentin, Hamelin, Chantal, Hueber, Yann, Kougbeadjo, Ayite, Larivière, Delphine, Larmande, Pierre, Lorenzo, Jonathan, Guillaume Martin, Monat, Cécile, Ndomassi, T., Ortega Abboud, Enrique, Pitollat, Bertrand, Sébastien RAVEL, Ranwez, Vincent, Rouard, Mathieu, Ruiz, E., Sabot, François, Sarah, Gautier, Sempere, Guilhem, Summo, Marilyne, This, Dominique, Tranchant-Dubreuil, Christine, Vallier, Félix, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biodiversity International, Université de Yaoundé I, Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA), and Université de Lyon (COMUE) more...
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C30 - Documentation et information ,U10 - Informatique, mathématiques et statistiques ,[SCCO.COMP]Cognitive science/Computer science ,U30 - Méthodes de recherche ,F30 - Génétique et amélioration des plantes - Abstract
International audience; In 2015, the South Green Bioinformatics Platform http://www.southgreen.fr/ is a network of 35 bioinformaticians from five biology research institutes working with two High - Performance Computing Data Centres to develop and use new tools for NGS/ Omic analytics of tropical and Mediterranean crops under projects studying relationsh ip between genetic diversity, agronomic performance and response to selection. South Green is affiliated to the South regional centre of the French Institute of Bioinformatics (the French node of the European research infrastructure, ELIXIR). This communit y and the HPC data centres are all located in Montpellier, which facilitates close collaboration and significant pooling to best meet the biologists' demands of our research units. Since 2004, we developed web - based applications with both generic and in - ho use components, for databases, analysis workflows and web interfaces, in order to: manage genetic and phenotypic information ( e.g. TropGeneDB), analyse molecular markers and genetic diversity ( e.g. SNiPlay), assemble transcriptomes ( e.g. ESTtik) map RNA - Se q ( e.g. ARCAD), annotate and compare genomes ( e.g. GNPAnnot), reconstruct evolutionary history of gene families by phylogenomics ( e.g. GreenPhyl). We also participate to the analysis of numerous crop species, that requires computing and storage facilities as well as interoperable information systems, such as rice ( e.g. OryGenesDB), wheat, sorghum, sugarcane, banana (Banana Genome Hub), palms, yam, coffee (CGH), rubber, cacao (CocoaGenDB), cotton, apple, grapevine, olive, eucalyptus, cassava. To face the dat a deluge, we must increase our analytics capabilities. We document our operation at both, administrator/ developer and user/ scientist level, to provide high quality services and reproducible research. We pool into working groups on key themes such as GBS, at both, developer (extreme pair programming) and user (interdisciplinary knowledge exchange) level. We provide training sessions each year. Finally, we implemented several instances of the Galaxy workflow manager and encapsulated our tools. These instanc es serve as a catalyst for massive NGS analyses but it remains to increase storage capacity and improve data management plans. (Résumé d'auteur) more...
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- 2015
17. MGIS: Managing banana (Musa spp.) genetic resources information and high-throughput genotyping data
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Ruas, Max, Guignon, Valentin, Sempere, Guilhem, Sardos, Julie, Hueber, Yann, Duvergey, H., Andrieu, A., Chase, Rachel, Jenny, Christophe, Hazekamp, T., Irish, B., Jelali, K., Adeka, J., Ayala-Silva, T., Chao, C.P., Daniells, J., Dowiya, B., Effa Effa, B., Gueco, L., Herradura, L., Ibobondji, L., Kempenaers, E., Kilangi, J., Muhangi, S., Ngo Xuan, P., Paofa, J., Pavis, Claude, Thiemele, D., Tossou, Christophe, Sandoval, Jorge A., Sutanto, A., Vangu Paka, G., Yi, G., Van Den Houwe, Ines, Roux, Nicolas, Rouard, Mathieu, Ruas, Max, Guignon, Valentin, Sempere, Guilhem, Sardos, Julie, Hueber, Yann, Duvergey, H., Andrieu, A., Chase, Rachel, Jenny, Christophe, Hazekamp, T., Irish, B., Jelali, K., Adeka, J., Ayala-Silva, T., Chao, C.P., Daniells, J., Dowiya, B., Effa Effa, B., Gueco, L., Herradura, L., Ibobondji, L., Kempenaers, E., Kilangi, J., Muhangi, S., Ngo Xuan, P., Paofa, J., Pavis, Claude, Thiemele, D., Tossou, Christophe, Sandoval, Jorge A., Sutanto, A., Vangu Paka, G., Yi, G., Van Den Houwe, Ines, Roux, Nicolas, and Rouard, Mathieu more...
- Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. more...
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- 2017
18. The South Green Bioinformatics platform, a comprehensive resource for crop genomics
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Ruiz, Manuel, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Tranchant-Dubreuil, Christine, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, De Lamotte, Frédéric, Larmande, Pierre, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, This, Dominique, Bocs, Stéphanie, Hueber, Yann, El Hassouni, Nordine, Martin, Guillaume, Gkanogiannis, Anestis, Ravel, Sébastien, Monat, Cécile, Tando, Ndomassi, Rouard, Mathieu, Ruiz, Manuel, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Tranchant-Dubreuil, Christine, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, De Lamotte, Frédéric, Larmande, Pierre, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, This, Dominique, Bocs, Stéphanie, Hueber, Yann, El Hassouni, Nordine, Martin, Guillaume, Gkanogiannis, Anestis, Ravel, Sébastien, Monat, Cécile, Tando, Ndomassi, and Rouard, Mathieu more...
- Abstract
Analysis and visualization of massive genomics datasets are an ongoing trend in plant sciences. The South Green Bioinformatics platform provides an ecosystem of tools that were originally developed as independent entities to fulfill the need for specific projects or crops, but have evolved over time to generic tools to comprehensively study crop genomics. We have built a large panel of public information systems dedicated to specialized datasets (markers, genes, gene families, transcriptomes, genotypes, phenotypes, etc.) and crop-specific resources called Genome Hubs. Target users of bioinformatic analytical workflows are usually divided between people who use command-line and those who do not. We addressed both categories by offering complementary solutions, like Galaxy-based and command-line applications. Various groups used the South Green infrastructure to obtain their data and results, and were able to publish high-quality biological information, on Coffee genome, Banana, Cocoa, African rice or large transcriptome resources. Tools developed for these studies are adaptable to a wide range of other organisms. more...
- Published
- 2017
19. Managing banana genetic resources and genomic information with the Triplet Drupal/Tripal/Chado [P0944]
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Guignon, Valentin, Ruas, Max, Droc, Gaëtan, Dereeper, Alexis, Sardos, Julie, Hueber, Yann, Dufayard, Jean-François, Roux, Nicolas, and Rouard, Mathieu
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F30 - Génétique et amélioration des plantes - Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, given the advances in NGS-based technologies that produce high-density genetic markers for a large number of samples at low cost. As SNP markers are being mapped on the reference genomes, it is important to develop interoperable system for managing both genomic data and genetic resources. The latter are often managed through bespoke information systems. The Musa Germplasm Information System (MGIS), the main banana genetic resource website, has recently been developed to address those needs in a convenient and flexible way. First of all, we decided to head for a generic database schema, such as CHADO, and to use a robust content management system such as Drupal as the web interface. The Tripal module provides the "glue" between these two parts and drastically reduces development time. Using this trio, we were able to quickly recreate in few months a complete and scalable site and expand it with new features. We now have a germplasm management system allowing collection browsing, and accession browsing, searching and ordering. Accession passport data have been enriched by geographical data, phenotyping characterization data, and information from diversity studies based on molecular markers and SNPs. As a first-use case, such genotyping studies allow linking with the Banana Genome Hub (BGH) website to explore these data in the genome context. (Texte intégral) more...
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- 2015
20. The South Green portal: A comprehensive resource for tropical and Mediterranean crop genomics
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Guignon, Valentin, Hueber, Yann, Rouard, Mathieu, Bocs, Stéphanie, Couvin, David, De Lamotte, Frédéric, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Gkanogiannis, Anestis, Hamelin, Chantal, Larivière, Delphine, Martin, Guillaume, Ortega, Enrique, Pitollat, Bertrand, Pointet, Stéphanie, Ruiz, Manuel, Gautier, Sarah, Summo, Marilyne, This, Dominique, Ravel, Sébastien, Larmande, Pierre, Monat, Cécile, Sabot, François, Tando, Ndomassi, Tranchant-Dubreuil, Christine, Sempere, Guilhem, Dereeper, Alexis, Guignon, Valentin, Hueber, Yann, Rouard, Mathieu, Bocs, Stéphanie, Couvin, David, De Lamotte, Frédéric, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Gkanogiannis, Anestis, Hamelin, Chantal, Larivière, Delphine, Martin, Guillaume, Ortega, Enrique, Pitollat, Bertrand, Pointet, Stéphanie, Ruiz, Manuel, Gautier, Sarah, Summo, Marilyne, This, Dominique, Ravel, Sébastien, Larmande, Pierre, Monat, Cécile, Sabot, François, Tando, Ndomassi, Tranchant-Dubreuil, Christine, Sempere, Guilhem, and Dereeper, Alexis more...
- Abstract
The South Green Web portal (http://www.southgreen.fr/) provides access to a large panel of public databases, analytical workflows and bioinformatics resources dedicated to the genomics of tropical and Mediterranean crops. The portal contains currently about 20 information systems and tools and targets a broad range of crops such as Banana, Cacao, Cassava, Coconut, Coffee, Grape, Rice and Sugarcane. more...
- Published
- 2016
21. A genome-wide association study on the seedless phenotype in banana (Musa spp.) reveals the potential of a selected panel to detect candidate genes in a vegetatively propagated crop
- Author
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Sardos, Julie, Rouard, Mathieu, Hueber, Yann, Cenci, Alberto, Hyma, Katie E., Van Den Houwe, Ines, Hribova, Eva, Courtois, Brigitte, Roux, Nicolas, Sardos, Julie, Rouard, Mathieu, Hueber, Yann, Cenci, Alberto, Hyma, Katie E., Van Den Houwe, Ines, Hribova, Eva, Courtois, Brigitte, and Roux, Nicolas more...
- Abstract
Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement. more...
- Published
- 2016
22. Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.)
- Author
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Lashermes, Philippe, primary, Hueber, Yann, additional, Combes, Marie-Christine, additional, Severac, Dany, additional, and Dereeper, Alexis, additional
- Published
- 2016
- Full Text
- View/download PDF
23. A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop
- Author
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Sardos, Julie, primary, Rouard, Mathieu, additional, Hueber, Yann, additional, Cenci, Alberto, additional, Hyma, Katie E., additional, van den Houwe, Ines, additional, Hribova, Eva, additional, Courtois, Brigitte, additional, and Roux, Nicolas, additional more...
- Published
- 2016
- Full Text
- View/download PDF
24. SNiPlay3: A web-based application for exploration and large scale analyses of genomic variations
- Author
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Dereeper, Alexis, Homa, Félix, Andres, Gwendoline, Sempere, Guilhem, Sarah, Gautier, Hueber, Yann, Dufayard, Jean François, Ruiz, Manuel, Dereeper, Alexis, Homa, Félix, Andres, Gwendoline, Sempere, Guilhem, Sarah, Gautier, Hueber, Yann, Dufayard, Jean François, and Ruiz, Manuel more...
- Abstract
SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr. more...
- Published
- 2015
25. SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations
- Author
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Dereeper, Alexis, primary, Homa, Felix, additional, Andres, Gwendoline, additional, Sempere, Guilhem, additional, Sarah, Gautier, additional, Hueber, Yann, additional, Dufayard, Jean-François, additional, and Ruiz, Manuel, additional more...
- Published
- 2015
- Full Text
- View/download PDF
26. Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids
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Combes, Marie-Christine, primary, Hueber, Yann, additional, Dereeper, Alexis, additional, Rialle, Stéphanie, additional, Herrera, Juan-Carlos, additional, and Lashermes, Philippe, additional
- Published
- 2015
- Full Text
- View/download PDF
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