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249 results on '"Gaspin, Christine"'

1. Massive detection of cryptic recessive genetic defects in dairy cattle mining millions of life histories

Author

Besnard, Florian, Guintard, Ana, Grohs, Cécile, Guzylack-Piriou, Laurence, Cano, Margarita, Escouflaire, Clémentine, Hozé, Chris, Leclerc, Hélène, Buronfosse, Thierry, Dutheil, Lucie, Jourdain, Jeanlin, Barbat, Anne, Fritz, Sébastien, Deloche, Marie-Christine, Remot, Aude, Gaussères, Blandine, Clément, Adèle, Bouchier, Marion, Contat, Elise, Relun, Anne, Plassard, Vincent, Rivière, Julie, Péchoux, Christine, Vilotte, Marthe, Eche, Camille, Kuchly, Claire, Charles, Mathieu, Boulling, Arnaud, Viard, Guillaume, Minéry, Stéphanie, Barbey, Sarah, Birbes, Clément, Danchin-Burge, Coralie, Launay, Frédéric, Mattalia, Sophie, Allais-Bonnet, Aurélie, Ravary, Bérangère, Millemann, Yves, Guatteo, Raphaël, Klopp, Christophe, Gaspin, Christine, Iampietro, Carole, Donnadieu, Cécile, Milan, Denis, Arcangioli, Marie-Anne, Boussaha, Mekki, Foucras, Gilles, Boichard, Didier, and Capitan, Aurélien

Published
2024
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4. Bounds Arc Consistency for Weighted CSPs

Author

Zytnicki, Matthias, Gaspin, Christine, de Givry, Simon, and Schiex, Thomas

Subjects
Computer Science - Artificial Intelligence
Abstract

The Weighted Constraint Satisfaction Problem (WCSP) framework allows representing and solving problems involving both hard constraints and cost functions. It has been applied to various problems, including resource allocation, bioinformatics, scheduling, etc. To solve such problems, solvers usually rely on branch-and-bound algorithms equipped with local consistency filtering, mostly soft arc consistency. However, these techniques are not well suited to solve problems with very large domains. Motivated by the resolution of an RNA gene localization problem inside large genomic sequences, and in the spirit of bounds consistency for large domains in crisp CSPs, we introduce soft bounds arc consistency, a new weighted local consistency specifically designed for WCSP with very large domains. Compared to soft arc consistency, BAC provides significantly improved time and space asymptotic complexity. In this paper, we show how the semantics of cost functions can be exploited to further improve the time complexity of BAC. We also compare both in theory and in practice the efficiency of BAC on a WCSP with bounds consistency enforced on a crisp CSP using cost variables. On two different real problems modeled as WCSP, including our RNA gene localization problem, we observe that maintaining bounds arc consistency outperforms arc consistency and also improves over bounds consistency enforced on a constraint model with cost variables.

Published
2014
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5. Oak genome reveals facets of long lifespan

Author

Plomion, Christophe, Aury, Jean-Marc, Amselem, Joëlle, Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur, Isabelle, Bartholomé, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Diévart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Bergès, Hélène, Bodénès, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, Da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima-Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Irène, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie-Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, and Salse, Jérôme

Published
2018
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6. A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling

Author

Eché, Camille, primary, Iampietro, Carole, additional, Birbes, Clément, additional, Dréau, Andreea, additional, Kuchly, Claire, additional, Di Franco, Arnaud, additional, Klopp, Christophe, additional, Faraut, Thomas, additional, Djebali, Sarah, additional, Castinel, Adrien, additional, Zytnicki, Matthias, additional, Denis, Erwan, additional, Boussaha, Mekki, additional, Grohs, Cécile, additional, Boichard, Didier, additional, Gaspin, Christine, additional, Milan, Denis, additional, and Donnadieu, Cécile, additional

Published
2023
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10. Structural and functional partitioning of bread wheat chromosome 3B

Author

Choulet, Frédéric, Alberti, Adriana, Theil, Sébastien, Glover, Natasha, Barbe, Valérie, Daron, Josquin, Pingault, Lise, Sourdille, Pierre, Couloux, Arnaud, Paux, Etienne, Leroy, Philippe, Mangenot, Sophie, Guilhot, Nicolas, Le Gouis, Jacques, Balfourier, Francois, Alaux, Michael, Jamilloux, Véronique, Poulain, Julie, Durand, Céline, Bellec, Arnaud, Gaspin, Christine, Safar, Jan, Dolezel, Jaroslav, Rogers, Jane, Vandepoele, Klaas, Aury, Jean-Marc, Mayer, Klaus, Berges, Hélène, Quesneville, Hadi, Wincker, Patrick, and Feuillet, Catherine

Published
2014

11. ASTERICS: A Tool for the ExploRation and Integration of omiCS data

Author

Maigné, Élise, Noirot, Céline, Mariette, Jérôme, Kesewaah, Yaa, Dejean, Sébastien, Guilmineau, Camille, Henry, Julien, Krebs, Arielle, Liaubet, Laurence, Mathevet, Fanny, Gaspin, Christine, Vialaneix, Nathalie, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bio-Informatique - Génotoul, 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), Institut National Polytechnique (Toulouse) (Toulouse INP), 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)-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)-Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-BioInfOmics, Plateforme de Biostatistique (Genotoul Biostat), 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 Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Région occitanie

Subjects
[INFO.INFO-WB]Computer Science [cs]/Web
Abstract

International audience

Published
2022
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12. metagWGS: a workflow to analyse short and long HiFi metagenomic reads Taxonomic profile HiFi vs Short reads assembly

Author

Fourquet, Joanna, Mainguy, Jean, Vienne, Maïna, Noirot, Céline, Martin, Pierre, Darbot, Vincent, Bouchez, Olivier, Castinel, Adrien, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Pascal, Géraldine, Hoede, Claire, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bio-Informatique - Génotoul, Université Fédérale Toulouse Midi-Pyrénées, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Société Française de Bioinformatique, GDR Bioinformatique Moléculaire, Institut Français de Bioinformatique, Institut national de recherche en sciences et technologies du numérique, FEDER funds (Programme Opérationnel FEDER-FSE_Midi-Pyrénées et Garonne 2014-2020), ATB_Biofilm funded by PNREST Anses, 2020/01/142, and Hoede, Claire

Subjects
bioInfOmics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience

Published
2022
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14. The benefits of long read HiFi sequencing for metabarcoding analysis

Author

Castinel, Adrien, Mainguy, Jean, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, Bouchez, Olivier, and Castinel, Adrien

Subjects
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Abstract

Today, the variable regions of 16S rRNA gene (V3-V4) is widely used to profile microbial communities, however the limited read lengths (460pb for the V3-V4 region) combined with the complexity of microbial samples makes it difficult to accurately identify bacterial strains and their abundance.The arrival PacBio Sequel II allow us to generate longer reads named “HiFi reads” using the circular consensus sequencing (CCS) mode, with an accuracy similar to the one observed on short reads. Therefore, we wanted to evaluate the taxonomic resolution using longer target region sequencing, such as, the full-length 16S (1.5kb) and 16S-23S genes (operon 4.5kb) and compared them to 16S RNA V3-V4 region. First, we have evaluated and implemented an extraction method in order to produce high size DNA fragment for long read sequencing while maintaining a good representativeness.Then, we conducted a comparative study of three PacBio protocols, the “Barcoded universal primers protocol” (BUP), the “Barcoded target specific primers protocol” (BTSP) and the “Barcoded overhang adapters protocol” (BOA) in order to perform CCS sequencing of the 16S, and 16S-23S genes on a microbial Community standard (mock) as well as pig faeces samples. Finally, we compared the taxonomic resolution between the 16S-23S, the 16S full length, and the 16sRNA V3V4. This work have been carried out within the framework of the SeqOccIn project (Sequencing Occitanie Innovation), supported by Get-PlaGe and Genotoul Bioinfo core facilities and financed by FEDER funds (Programme Opérationnel FEDER-FSE_Midi-Pyrénées et Garonne 2014-2020).

Published
2022

15. Implementation of new methods for metagenomics analysis using PacBio HiFi sequencing

Author

Castinel, Adrien, Mainguy, Jean, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, Bouchez, Olivier, and iampietro, carole

Subjects
[SDV] Life Sciences [q-bio], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

The variable regions of 16S rRNA gene is widely used to profile microbial communities, however the limited read lengths (e.g 460pb for the V3-V4 region) combined with the complexity of microbial samples makes it difficult to accurately identify bacterial strains and their abundance. The arrival PacBio Sequel II sequencer allow us to generate longer reads named "HiFi reads" using the circular consensus sequencing (CCS) mode, with an accuracy similar to the one observed for short reads sequencers.

Published
2022

16. metagWGS: a workflow to analyse short and long HiFi metagenomic reads

Author

Fourquet, Joanna, Vienne, Maïna, Mainguy, Jean, Darbot, Vincent, Martin, Pierre, Bouchez, Olivier, Castinel, Adrien, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Noirot, Céline, Pascal, Géraldine, Hoede, Claire, Hoede, Claire, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bio-Informatique - Génotoul, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), 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), and 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience

Published
2022

17. Strengths and limits of long read metabarcoding

Author

Mainguy, Jean, Castinel, Adrien, Bouchez, Olivier, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, and Pascal, Géraldine

Subjects
16-23S, metabarcoding, HiFi long reads, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Metabarcoding is the large-scale taxonomic identification of complex environmental samples via analysis of DNA reads of one marker gene. Different marker genes are used, the 16S rRNA gene is mainly used to identify bacteria. We conducted a comparative study to understand the limitations and strengths of PacBio HiFi long read sequencing technology for metabarcoding analyses. We performed the same analyses on two types of datasets. A commercial ZymoBIOMICS mock community consisting of eight bacteria and 32 samples containing pig fecal microbiota from the ExpomycoPig project. We focused on the 16S-23S rRNA gene operon and sequenced 3 types of amplicons by metabarcoding: the V3-V4 region of the 16S rRNA, the full-length 16S rRNA gene and the full-length 16S-23S gene operon. We observe that by using HIFI long reads we increase the specificity of sample characterization. But when we analyze the 16S-23S amplicons, the specificity increases within the limit of the availability of the sequence in the databases that are much less comprehensive than the databases containing only 16S data. A strategy of affiliating 16S-23S amplicons on complementary databases (Silva 16S and 23S and a custom 16S-23S operon database) improves microbial identifications.

Published
2022

18. Structural variants detection and de novo genome assembly of a maize line

Author

Eché, Camille, Birbes, Clement, Iampietro, Carole, Di Franco, Arnaud, Dreau, Andreea, Kuchly, Claire, Klopp, Christophe, Faraut, Thomas, Zytnicki, Matthias, Denis, Erwan, Praud, Sebastien, Joets, Johann, Vitte, Clémentine, Charcosset, Alain, Gaspin, Christine, Milan, Denis, Donnadieu, Cecile, and iampietro, carole

Subjects
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Characterizing the genomic diversity of species is critical to understand the molecular origin of phenotypic variations. Whole genome sequence assemblies at the chromosome scale with low amount of missing data are critical resources for answering such questions. Our aim is to explore combination of technologies to answer those questions, and to find the best one. Using a specific Maize line, we have tested different sequencing applications to build a "high quality genome" and identify a large collection of genome variants. Here we demonstrate that the use of HIFI reads combined with Hi-C and Linked-reads generate a chromosome-scale genome assembly with a better contiguity than the reference genome B73. Moreover we show, that PacBio CLR reads allow a wide detection of structural variants of the genomes.

Published
2022

20. Preliminary results from Nanopore Q20+ sequencing

Author

Kuchly, Claire, Sabban, Jules, Darnige, Eden, Eché, Camille, Suin, Amandine, Vandecasteele, Céline, Birbes, Clement, Dreau, Andreea, Klopp, Christophe, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Salin, Gérald, Lopez-Roques, Céline, Kuchly, Claire, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract

International audience

Published
2022

21. Genetic algorithms for genetic mapping

Author

Gaspin, Christine, Schiex, Thomas, Goos, G., editor, Hartmanis, J., editor, van Leeuwen, J., editor, Hao, Jin-Kao, editor, Lutton, Evelyne, editor, Ronald, Edmund, editor, Schoenauer, Marc, editor, and Snyers, Dominique, editor

Published
1998
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26. Benefits of PacBio HiFi long reads for metagenomic whole genome analysis

Author

Castinel, Adrien, Mainguy, Jean, Bouchez, Olivier, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cecile, Pascal, Géraldine, Hoede, Claire, Mainguy, Jean, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GeT-PlaGe, US 1426, Genotoul, INRAE, 31320 Castanet-Tolosan, France, MIAT, PF Bioinfo GenoToul, Université de Toulouse, INRAE, Chemin de Borde Rouge, 31320 Castanet-Tolosan, France, and GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Chemin de Borde Rouge, 31320 Castanet Tolosan, France

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

International audience; Whole metagenomics analysis aim to provide an overview of the biodiversity and the functions of bacterial communities. Currently, those analysis are performed on Illumina short read sequencers that provide the advantage of generating less than 1% sequencing error. The arrival of the HiFi technology (PacBio Sequel II) allow us to sequence long read fragments of several Kb with a low error rate. One of the aim of the SeqOccIn project (Sequencing Occitanie Innovation, https://get.genotoul.fr/seqoccin/) is to acquire expertise in metagenomics to better characterize microbial communities inside complex matrices. In the framework of this project, we developed the metagenomics shotgun protocol on the PacBio Sequel II sequencer and carry out a comparative study of the assemblies obtained with PacBio long reads and Illumina short reads data.

Published
2021

27. De novo assembling 19 maize inbred lines of the European germplasm

Author

Iampietro, Carole, Eché, Camille, Birbes, Clement, Dreau, Andreea, Denis, Erwan, Kuchly, Claire, Klopp, Christophe, Di Franco, Arnaud, Faraut, Thomas, Zytnicki, Matthias, Joets, Johann, Vitte, Clémentine, Charcosset, Alain, Gaspin, Christine, Milan, Denis, Donnadieu, Cecile, and iampietro, carole

Subjects
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

Background and objectives Characterizing the genomic diversity of maize is critical to understand the molecular origin of structural variation, and is a prerequisite to underpin the functional variation underlying phenotypic variation. Whole genome sequence assemblies at the chromosome scale with low amount of missing data are critical resources for answering such questions. Whole genome sequence assemblies are now available for several maize inbred lines, but this is still missing for a number of key founders used in European maize breeding programs. This concerns the dent genetic pool and the European specific flint genetic group. Therefore, we have established a list of 13 priority lines for de novo sequencing as part of the SeqOccIn project.

Published
2021

28. De novo assembly of bovine genome using PacBio applications

Author

Eché, Camille, Birbes, Clément, Iampietro, Carole, Dréau, Andreea, Kuchly, Claire, Klopp, Christophe, Di Franco, Arnaud, Faraut, Thomas, Zytnicki, Matthias, Denis, Erwan, Fritz, Sébastien, Boussaha, Mekki, Grohs, Cécile, Boichard, Didier, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, and iampietro, carole

Subjects
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Background and objectives GeT-PlaGe is a genomic core facility which provides technologies and expertise in genome sequencing to academic and private research teams. The SeqOccIn (Sequencing Occitanie Innovation) project, supported by Get-PlaGe and Genotoul Bioinfo platforms, was selected by the Occitanie Region as part of the call for projects "Regional Research and Innovation Platforms". The main objective is to acquire expertise on the optimal combination of long fragment sequencing technologies and associated applications to better characterize complex genomes in agronomical field: from SNP and structural variations detection, to the production of a high quality assemblies. Therefore, to obtain the best genome using PacBio datas, several de novo assembly strategies on a Charolais bovine will be presented : CLR datas only, CCS datas only and trio binning approach. In this poster, we highlight biologicial and bioinformatic aspects taking into account the scientific purpose and different constraints (time, budget, samples qualities). For this work, we sequenced the same individual (offspring bovine) with different applications: PacBio, ONT and Hi-C, and parents with classical short reads (2x150 pb Illumina).

Published
2021

30. Communication et connaissance

Author

Aussenac, Nathalie, Balacheff, Nicolas, Bazet, Isabelle, Beaudouin-Lafon, Michel, Beauvillain, Pierre, Bourcier, Danièle, Bourigault, Didier, Bréchignac, Catherine, Breton, Philippe, Caelen, Jean, Cara, Francesco, Chappert, Claude, Charlet, Jean, Chavel, Pierre, Decoster, Didier, de Rougemont, Michel, de Terssac, Gilbert, Dieng-Kuntz, Rose, Dollfus, Philippe, Fdida, Serge, Flandrin, Patrick, Gallinari, Patrick, Ganascia, Jean-Gabriel, Garnero, Line, Gaspin, Christine, Gaudel, Marie-Claude, Hoc, Jean-Michel, Jacob, Christian, Jorrand, Philippe, Loiseau, Gérard, Munoz-Yague, Antonio, Pierrel, Jean-Marie, Plateau, Brigitte, Quéré, Raymond, Rastier, François, Rolland, Paul-Alain, Saillard, Joseph, Salaün, Jean-Michel, Sanchez, Jean Pierre, Scholl, Michel, Trystram, Denis, and Ganascia, Jean-Gabriel

Subjects
TIC, informatique, télécommunication, internet, Library, Information & Communication sciences, donnée, JFD, SOC052000, web, information, modélisation
Abstract

Depuis 25 ans, les technologies de l’information et de communication ont transformé le monde. En quelques années, le commerce, la finance, les échanges, l’école, le travail, la culture, la politique, etc. se sont totalement modifiés du fait de leur développement. Qu’on se remémore quelques-unes des étapes les plus marquantes de ces évolutions : apparition des mini puis des micro-ordinateurs, nouvelles interfaces avec utilisation de la souris et métaphore du bureau, essor des hypermédia, popularisation du Web, nomadisme généralisé, informatique vestimentaire, intelligence d’ambiance... Les changements ont été imaginés, conçus, développés, expérimentés dans des laboratoires de recherche. Partout, la recherche a pris, et continue de prendre, une part déterminante. Or, il est parfois difficile de discerner ce qui relève de la recherche fondamentale et du travail universitaire, de ce qui correspond à l’innovation industrielle. Qu’est-ce qui distingue la « R. et D. » — la recherche et développement Industriel — de la recherche universitaire ? Quelle part cette dernière prend-elle exactement dans l’innovation ? Quel rôle sera-t-elle amenée à jouer dans les prochaines années ? Telles sont les questions auxquelles nous avons voulu répondre en publiant un ouvrage destiné aux ingénieurs, aux chercheurs, aux décideurs et, plus généralement, à l’honnête homme du début du xxie siècle qui souhaite comprendre le sens des évolutions technologiques actuelles.

Published
2020

31. Modélisations

Author

Gaudel, Marie-Claude, Flandrin, Patrick, Gaspin, Christine, and Plateau, Brigitte

Subjects
TIC, informatique, télécommunication, internet, Library, Information & Communication sciences, donnée, JFD, SOC052000, web, information, modélisation
Abstract

3.1. Logiciels : les objets à l’épreuve des faits (Marie-Claude Gaudel) Les applications informatiques, ainsi que les machines et systèmes qui leur servent de support sont de plus en plus complexes. Dans ce contexte, il devient très difficile de développer et de garantir les logiciels. La réalisation de logiciels de qualité est à la fois un objectif économique essentiel et un axe de recherche de longue haleine – le génie logiciel – qui combine des activités très théoriques et très appliquées....

Published
2020

32. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis

Author

Iampietro, Carole, Eché, Camille, Castinel, Adrien, Serre, Rémy-Félix, Klopp, Christophe, Denis, Erwan, Bouchez, Olivier, Kuchly, Claire, Vandecasteele, Céline, BROHA, Amandine, THERVILLE, Romain, Di Franco, Arnaud, Djebali Quelen, Sarah, DREAU, Andreea, Hoede, Claire, KOROVINA, Oleksandra, BIRBES, CLEMENT, Laborie, Didier, Mainguy, Jean, Noirot, Céline, Salin, Gerald, Terzian, Paul, Trotard, Marie-Stéphane, Boichard, Didier, Boussaha, Mekki, Grohs, Cécile, Charcosset, Alain, Belcram, Harry, Joets, Johann, Combes, Sylvie, Pascal, Géraldine, Pitel, Frederique, Leroux, Sophie, Riquet, Juliette, Demars, Julie, Tosser-Klopp, Gwenola, Vitte, Clémentine, Iannuccelli, Nathalie, Lluch, Jérôme, Lopez-Roques, Celine, Faraut, Thomas, Zytnicki, Matthias, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), FEDER-Région Occitanie, 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)-Université Toulouse III - Paul Sabatier (UT3), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

33. Improving microbial taxonomic profiling with long read technologies

Author

Mainguy, Jean, Castinel, Adrien, Bouchez, Olivier, Combes, Sylvie, Iampietro, Carole, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Hoede, Claire, Pascal, Géraldine, Pascal, Géraldine, and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience

Published
2020

37. Modélisations

Author

Gaudel, Marie-Claude, primary, Flandrin, Patrick, additional, Gaspin, Christine, additional, and Plateau, Brigitte, additional

Published
2006
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39. Identification of genomic regions for high-resolution taxonomic profiling using long-read sequencing technology

Author

Mainguy, Jean, Bouchez, Olivier, Castinel, Adrien, Combes, Sylvie, Gaspin, Christine, Milan, Denis, Donnadieu, Cecile, Iampietro, Carole, Hoede, Claire, Pascal, Géraldine, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III - Paul Sabatier (UT3), and 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)

Subjects
genomic, identification, bioinformatic, taxonomic, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], ComputingMilieux_MISCELLANEOUS, Autre (Sciences du Vivant)
Abstract

National audience

Published
2019

40. Whole metagenome analysis with metagWGS

Author

Fourquet, Joanna, Chaubet, Adeline, Chiapello, Hélène, Gaspin, Christine, Haenni, Marisa, Klopp, Christophe, Lupo, Agnese, Mainguy, Jean, Noirot, Celine, Rochegue, Tony, Zytnicki, Matthias, Ferry, Tristan, Hoede, Claire, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), International Center for Infectiology Research, Labex ECOFECT, Université Toulouse III - Paul Sabatier (UT3), and 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)

Subjects
metagenomics, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, gut microbiota, workflow, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2019

41. A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers

Author

Laurent, Valerie, Wajnberg, Eric, Mangin, Brigitte, Schiex, Thomas, Gaspin, Christine, and Vanlerberghe-Masutti, Flavie

Subjects
Wasps -- Genetic aspects, Chromosome mapping -- Research, Genetic markers -- Research, Linkage (Genetics) -- Research, Biological sciences
Abstract

Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three [F.sub.2] populations. These populations were composed of the haploid male progeny of several virgin [F.sub.1] females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM.

Published
1998

42. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Author

Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, Couloux, Arnaud, Déhais, Patrice, Deléage, Gilbert, Duclert, Aymeric, Echeverria, Manuel, Eschbach, Aimée, Falconet, Denis, Filippi, Ghislain, Gaspin, Christine, Geourjon, Christophe, Grienenberger, Jean-Michel, Houlné, Guy, Jamet, Elisabeth, Lechauve, Frédéric, Leleu, Olivier, Leroy, Philippe, Mache, Régis, Meyer, Christian, Nedjari, Hafed, Negrutiu, Ioan, Orsini, Valérie, Peyretaillade, Eric, Pommier, Cyril, Raes, Jeroen, Risler, Jean-Loup, Rivière, Stéphane, Rombauts, Stéphane, Rouzé, Pierre, Schneider, Michel, Schwob, Philippe, Small, Ian, Soumayet-Kampetenga, Ghislain, Stankovski, Darko, Toffano, Claire, Tognolli, Michael, Caboche, Michel, and Lecharny, Alain

Published
2005

44. Oak genome reveals facets of long lifespan

Author

Leroy, Thibault, Murat, Florent, Duplessis, Sébastien, Faye, Sébastien, Francillonne, Nicolas, Labadie, Karine, Le Provost, Grégoire, Lesur Kupin, Isabelle, Bartholome, Jérôme, Faivre-Rampant, Patricia, Kohler, Annegret, Leplé, Jean-Charles, Chantret, Nathalie, Chen, Jun, Dievart, Anne, Alaeitabar, Tina, Barbe, Valérie, Belser, Caroline, Berges, Helene, Bodenes, Catherine, Bogeat-Triboulot, Marie-Béatrice, Bouffaud, Marie-Lara, Brachi, Benjamin, Chancerel, Emilie, Cohen, David, Couloux, Arnaud, Da Silva, Corinne, Dossat, Carole, Ehrenmann, François, Gaspin, Christine, Grima-Pettenati, Jacqueline, Guichoux, Erwan, Hecker, Arnaud, Herrmann, Sylvie, Hugueney, Philippe, Hummel, Iréne, Klopp, Christophe, Lalanne, Céline, Lascoux, Martin, Lasserre, Eric, Lemainque, Arnaud, Desprez-Loustau, Marie Laure, Luyten, Isabelle, Madoui, Mohammed-Amin, Mangenot, Sophie, Marchal, Clémence, Maumus, Florian, Mercier, Jonathan, Michotey, Célia, Panaud, Olivier, Picault, Nathalie, Rouhier, Nicolas, Rué, Olivier, Rustenholz, Camille, Salin, Franck, Soler, Marçal, Tarkka, Mika, Velt, Amandine, Zanne, Amy E., Martin, Francis, Wincker, Patrick, Quesneville, Hadi, Kremer, Antoine, Salse, Jerome, Plomion, Christophe, Aury, Jean-Marc, and Amselem, Joelle

Subjects
Forestry, Genomics, Plant evolution, Plant Immunity, Sequencing
Abstract

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Published
2018

46. Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

Author

Polonais, Valérie, primary, Niehus, Sebastian, additional, Wawrzyniak, Ivan, additional, Franchet, Adrien, additional, Gaspin, Christine, additional, Belkorchia, Abdel, additional, Reichstadt, Matthieu, additional, Belser, Caroline, additional, Labadie, Karine, additional, Couloux, Arnaud, additional, Delbac, Frédéric, additional, Peyretaillade, Eric, additional, and Ferrandon, Dominique, additional

Published
2019
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47. Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

Author

Carpousis Agamemnon J, Brucato Nicolas, Rinaldi Dana, Moisan Annick, Phok Kounthéa, Gaspin Christine, and Clouet-d'Orval Béatrice

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs. Results Using a combination of in silico and experimental approaches, we identified and characterized novel P. abyssi ncRNAs transcribed from 12 intergenic regions, ten of which are conserved throughout the Thermococcales. Several of them accumulate in the late-exponential phase of growth. Analysis of the genomic context and sequence conservation amongst related thermococcal species revealed two novel P. abyssi ncRNA families. The CRISPR family is comprised of crRNAs expressed from two of the four P. abyssi CRISPR cassettes. The 5'UTR derived family includes four conserved ncRNAs, two of which have features similar to known bacterial riboswitches. Several of the novel ncRNAs have sequence similarities to orphan OrfB transposase elements. Based on RNA secondary structure predictions and experimental results, we show that three of the twelve ncRNAs include Kink-turn RNA motifs, arguing for a biological role of these ncRNAs in the cell. Furthermore, our results show that several of the ncRNAs are subjected to processing events by enzymes that remain to be identified and characterized. Conclusions This work proposes a revised annotation of CRISPR loci in P. abyssi and expands our knowledge of ncRNAs in the Thermococcales, thus providing a starting point for studies needed to elucidate their biological function.

Published
2011
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48. Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function

Author

Lescure Bernard, Rami Jean-François, and Gaspin Christine

Subjects
Botany, QK1-989
Abstract

Abstract Background Short interstitial telomere motifs (telo boxes) are short sequences identical to plant telomere repeat units. They are observed within the 5' region of several genes over-expressed in cycling cells. In synergy with various cis-acting elements, these motifs participate in the activation of expression. Here, we have analysed the distribution of telo boxes within Arabidopsis thaliana and Oryza sativa genomes and their association with genes involved in the biogenesis of the translational apparatus. Results Our analysis showed that the distribution of the telo box (AAACCCTA) in different genomic regions of A. thaliana and O. sativa is not random. As is also the case for plant microsatellites, they are preferentially located in the 5' flanking regions of genes, mainly within the 5' UTR, and distributed as a gradient along the direction of transcription. As previously reported in Arabidopsis, a conserved topological association of telo boxes with site II or TEF cis-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in O. sativa. Such a conserved promoter organization can be found in other genes involved in the biogenesis of the translational machinery including rRNA processing proteins and snoRNAs. Strikingly, the association of telo boxes with site II motifs or TEF boxes is conserved in promoters of genes harbouring snoRNA clusters nested within an intron as well as in the 5' flanking regions of non-intronic snoRNA genes. Thus, the search for associations between telo boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters. Conclusions The data reported in this work support the model previously proposed for the spreading of telo boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of telo boxes with site II or TEF cis-acting elements appears to be an essential feature of plant genes involved in the biogenesis of ribosomes and clearly indicates that most plant snoRNAs are RNA pol II products.

Published
2010
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49. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

Author

Decatur Wayne A, Marck Christian, Gaspin Christine, Grosjean Henri, and de Crécy-Lagard Valérie

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes. Results By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions. Conclusion The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation.

Published
2008
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50. LeARN: a platform for detecting, clustering and annotating non-coding RNAs

Author

Schiex Thomas, Gaspin Christine, Noirot Céline, and Gouzy Jérôme

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs) in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules. Results LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation. Conclusion This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN

Published
2008
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