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206 results on '"Noirot, Céline"'

5. The BioMart community portal: an innovative alternative to large, centralized data repositories.

Author

Smedley, Damian, Haider, Syed, Durinck, Steffen, Pandini, Luca, Provero, Paolo, Allen, James, Arnaiz, Olivier, Awedh, Mohammad Hamza, Baldock, Richard, Barbiera, Giulia, Bardou, Philippe, Beck, Tim, Blake, Andrew, Bonierbale, Merideth, Brookes, Anthony J, Bucci, Gabriele, Buetti, Iwan, Burge, Sarah, Cabau, Cédric, Carlson, Joseph W, Chelala, Claude, Chrysostomou, Charalambos, Cittaro, Davide, Collin, Olivier, Cordova, Raul, Cutts, Rosalind J, Dassi, Erik, Di Genova, Alex, Djari, Anis, Esposito, Anthony, Estrella, Heather, Eyras, Eduardo, Fernandez-Banet, Julio, Forbes, Simon, Free, Robert C, Fujisawa, Takatomo, Gadaleta, Emanuela, Garcia-Manteiga, Jose M, Goodstein, David, Gray, Kristian, Guerra-Assunção, José Afonso, Haggarty, Bernard, Han, Dong-Jin, Han, Byung Woo, Harris, Todd, Harshbarger, Jayson, Hastings, Robert K, Hayes, Richard D, Hoede, Claire, Hu, Shen, Hu, Zhi-Liang, Hutchins, Lucie, Kan, Zhengyan, Kawaji, Hideya, Keliet, Aminah, Kerhornou, Arnaud, Kim, Sunghoon, Kinsella, Rhoda, Klopp, Christophe, Kong, Lei, Lawson, Daniel, Lazarevic, Dejan, Lee, Ji-Hyun, Letellier, Thomas, Li, Chuan-Yun, Lio, Pietro, Liu, Chu-Jun, Luo, Jie, Maass, Alejandro, Mariette, Jerome, Maurel, Thomas, Merella, Stefania, Mohamed, Azza Mostafa, Moreews, Francois, Nabihoudine, Ibounyamine, Ndegwa, Nelson, Noirot, Céline, Perez-Llamas, Cristian, Primig, Michael, Quattrone, Alessandro, Quesneville, Hadi, Rambaldi, Davide, Reecy, James, Riba, Michela, Rosanoff, Steven, Saddiq, Amna Ali, Salas, Elisa, Sallou, Olivier, Shepherd, Rebecca, Simon, Reinhard, Sperling, Linda, Spooner, William, Staines, Daniel M, Steinbach, Delphine, Stone, Kevin, Stupka, Elia, Teague, Jon W, Dayem Ullah, Abu Z, Wang, Jun, and Ware, Doreen

Subjects
Humans, Neoplasms, Proteomics, Genomics, Internet, Database Management Systems, Developmental Biology, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Published
2015

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. Study of the colonic epithelial-mesenchymal dialogue through establishment of two activated or not mesenchymal cell lines: Activated and resting ones differentially modulate colonocytes in co-culture

Author

Plaisancié, Pascale, primary, Buisson, Charline, additional, Fouché, Edwin, additional, Martin, Pierre, additional, Noirot, Céline, additional, Maslo, Claire, additional, Dupuy, Jacques, additional, Guéraud, Françoise, additional, and Pierre, Fabrice, additional

Published
2022
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13. 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. Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly

Author

Nieberding, Caroline M., primary, Beldade, Patrícia, additional, Baumlé, Véronique, additional, San Martin, Gilles, additional, Arun, Alok, additional, Lognay, Georges, additional, Montagné, Nicolas, additional, Bastin-Héline, Lucie, additional, Jacquin-Joly, Emmanuelle, additional, Noirot, Céline, additional, Klopp, Christophe, additional, and Visser, Bertanne, additional

Published
2022
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15. SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species

Author

Demange, Pascal, primary, Joly, Etienne, primary, Marcoux, Julien, primary, Zanon, Patrick RA, additional, Listunov, Dymytrii, additional, Rullière, Pauline, additional, Barthes, Cécile, additional, Noirot, Céline, additional, Izquierdo, Jean-Baptiste, additional, Rozié, Alexandrine, additional, Pradines, Karen, additional, Hee, Romain, additional, de Brito, Maria Vieira, additional, Marcellin, Marlène, additional, Serre, Remy-Felix, additional, Bouchez, Olivier, additional, Burlet-Schiltz, Odile, additional, Oliveira, Maria Conceição Ferreira, additional, Ballereau, Stéphanie, additional, Bernardes-Génisson, Vania, additional, Maraval, Valérie, additional, Calsou, Patrick, additional, Hacker, Stephan M, additional, Génisson, Yves, additional, Chauvin, Remi, additional, and Britton, Sébastien, additional

Published
2022
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16. Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus

Author

Payton, Laura, Noirot, Céline, Kim, Last, Grigor, Jordan, Hüppe, Lukas, Conway, David V. P., Dannemeyer, Mona, Suin, Amandine, Meyer, Bettina, Payton, Laura, Noirot, Céline, Kim, Last, Grigor, Jordan, Hüppe, Lukas, Conway, David V. P., Dannemeyer, Mona, Suin, Amandine, and Meyer, Bettina

Abstract

The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic spe-cies with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food sup-ply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N. Atlantic ecosystem. While diapause mechanisms are mainly studied in terrestrial arthropods, specifically on laboratory model species, such as the fruit fly Drosophila, the molecular investigations of annual rhythms in wild marine species remain fragmentary. Here we performed a rigorous year-l ong monthly sampling campaign of C. finmarchicus in a Scottish Loch (UK; 56.45°N, 5.18°W) to generate an annual transcriptome. The mRNA of 36 samples (monthly triplicate of 25 individuals) have been deeply sequenced with an average depth of 137 ± 4 million reads (mean ± SE) per sample, aligned to the reference transcriptome, and filtered. We detail the quality assessment of the datasets and provide a high- quality resource for the investigation of wild annual transcriptomic rhythms (35,357 components) in a key diapausing zooplanktonic species.

Published
2022

17. Author response: SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species

Author

Demange, Pascal, primary, Joly, Etienne, primary, Marcoux, Julien, primary, Zanon, Patrick RA, additional, Listunov, Dymytrii, additional, Rullière, Pauline, additional, Barthes, Cécile, additional, Noirot, Céline, additional, Izquierdo, Jean-Baptiste, additional, Rozié, Alexandrine, additional, Pradines, Karen, additional, Hee, Romain, additional, de Brito, Maria Vieira, additional, Marcellin, Marlène, additional, Serre, Remy-Felix, additional, Bouchez, Olivier, additional, Burlet-Schiltz, Odile, additional, Oliveira, Maria Conceição Ferreira, additional, Ballereau, Stéphanie, additional, Bernardes-Génisson, Vania, additional, Maraval, Valérie, additional, Calsou, Patrick, additional, Hacker, Stephan M, additional, Génisson, Yves, additional, Chauvin, Remi, additional, and Britton, Sébastien, additional

Published
2022
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19. 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

24. SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species

Author

Demange, Pascal, primary, Joly, Etienne, additional, Marcoux, Julien, additional, Zanon, Patrick R. A., additional, Listunov, Dymytrii, additional, Rullière, Pauline, additional, Barthes, Cécile, additional, Noirot, Céline, additional, Izquierdo, Jean-Baptiste, additional, Pradines, Karen, additional, Hee, Romain, additional, de Brito, Maria Vieira, additional, Marcellin, Marlène, additional, Serre, Rémi-Félix, additional, Bouchez, Olivier, additional, Burlet-Schiltz, Odile, additional, Oliveira, Maria Conceição Ferreira, additional, Ballereau, Stéphanie, additional, Bernardes-Génisson, Vania, additional, Maraval, Valérie, additional, Calsou, Patrick, additional, Hacker, Stephan M., additional, Génisson, Yves, additional, Chauvin, Remi, additional, and Britton, Sébastien, additional

Published
2021
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26. Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands

Author

Bossaert, Madeleine, primary, Pipier, Angélique, additional, Riou, Jean-Francois, additional, Noirot, Céline, additional, Nguyên, Linh-Trang, additional, Serre, Remy-Felix, additional, Bouchez, Olivier, additional, Defrancq, Eric, additional, Calsou, Patrick, additional, Britton, Sébastien, additional, and Gomez, Dennis, additional

Published
2021
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27. Author response: Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands

Author

Bossaert, Madeleine, primary, Pipier, Angélique, additional, Riou, Jean-Francois, additional, Noirot, Céline, additional, Nguyên, Linh-Trang, additional, Serre, Remy-Felix, additional, Bouchez, Olivier, additional, Defrancq, Eric, additional, Calsou, Patrick, additional, Britton, Sébastien, additional, and Gomez, Dennis, additional

Published
2021
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28. Whole metagenome analysis with metagWGS

Author

Fourquet, Joanna, Noirot, Céline, Klopp, Christophe, Pinton, Philippe, Combes, Sylvie, Hoede, Claire, Pascal, Géraldine, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Pascal, Géraldine

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

International audience; Whole DNA shotgun sequencing of environmental samples allows to study their taxonomic composition and their functional profiles. However, the biological process from collecting data to sequencing and bioinformatics analysis are still very tricky [1].We are developing a complete, scalable, easy-to-use and reproducible workflow, MetagWGS, with Nextflow [2] and Singularity [3] that processes short Illumina reads from shotgun metagenomics data. It delivers (i) contig assemblies, (ii) syntactic and functional annotations of genes, (iii) taxonomic affiliations of reads and contigs, (iv) count table of reads per genes and (v) contig binning to obtain metagenome species.The workflow begins by preprocessing steps that clean adapters, low quality reads and the host reads. We control the quality of the reads with FastQC [4]. The taxonomic classification of reads uses Kaiju [5] in order to have a first overview of reads. The assembly step uses metaSPAdes [6] or megahit [7] to generate contigs for each sample. These contigs are annotated by Prokka [8]. Then, with CD-HIT [9] we remove redundancy and generate a gene catalog by clustering ORFs at sample level and globally with a 95% sequence identity cutoff. We map reads back to contigs and we use featureCounts [10] to count the reads overlapping annotated genes. The raw count table gathers the number of reads aligned on each gene for each sample. We use DIAMOND [11] for the taxonomic affiliation of contigs versus nr database. We include contig binning processes from nf-core/mag pipeline. We generate a single result report with MultiQC [12].MetagWGS is available on https://forgemia.inra.fr/genotoul-bioinfo/metagwgs. We will apply it on sequences from ExpoMycoPig project that aims to study gut microbiota of pigs exposed to mycotoxins [13].

Published
2020

30. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
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31. The Medicago genome provides insight into the evolution of rhizobial symbioses

Author

Young, Nevin D., Debellé, Frédéric, Oldroyd, Giles E. D., Geurts, Rene, Cannon, Steven B., Udvardi, Michael K., Benedito, Vagner A., Mayer, Klaus F. X., Gouzy, Jérôme, Schoof, Heiko, Van de Peer, Yves, Proost, Sebastian, Cook, Douglas R., Meyers, Blake C., Spannagl, Manuel, Cheung, Foo, De Mita, Stéphane, Krishnakumar, Vivek, Gundlach, Heidrun, Zhou, Shiguo, Mudge, Joann, Bharti, Arvind K., Murray, Jeremy D., Naoumkina, Marina A., Rosen, Benjamin, Silverstein, Kevin A. T., Tang, Haibao, Rombauts, Stephane, Zhao, Patrick X., Zhou, Peng, Barbe, Valérie, Bardou, Philippe, Bechner, Michael, Bellec, Arnaud, Berger, Anne, Bergès, Hélène, Bidwell, Shelby, Bisseling, Ton, Choisne, Nathalie, Couloux, Arnaud, Denny, Roxanne, Deshpande, Shweta, Dai, Xinbin, Doyle, Jeff J., Dudez, Anne-Marie, Farmer, Andrew D., Fouteau, Stéphanie, Franken, Carolien, Gibelin, Chrystel, Gish, John, Goldstein, Steven, González, Alvaro J., Green, Pamela J., Hallab, Asis, Hartog, Marijke, Hua, Axin, Humphray, Sean J., Jeong, Dong-Hoon, Jing, Yi, Jöcker, Anika, Kenton, Steve M., Kim, Dong-Jin, Klee, Kathrin, Lai, Hongshing, Lang, Chunting, Lin, Shaoping, Macmil, Simone L., Magdelenat, Ghislaine, Matthews, Lucy, McCorrison, Jamison, Monaghan, Erin L., Mun, Jeong-Hwan, Najar, Fares Z., Nicholson, Christine, Noirot, Céline, O’Bleness, Majesta, Paule, Charles R., Poulain, Julie, Prion, Florent, Qin, Baifang, Qu, Chunmei, Retzel, Ernest F., Riddle, Claire, Sallet, Erika, Samain, Sylvie, Samson, Nicolas, Sanders, Iryna, Saurat, Olivier, Scarpelli, Claude, Schiex, Thomas, Segurens, Béatrice, Severin, Andrew J., Sherrier, Janine D., Shi, Ruihua, Sims, Sarah, Singer, Susan R., Sinharoy, Senjuti, Sterck, Lieven, Viollet, Agnès, Wang, Bing-Bing, Wang, Keqin, Wang, Mingyi, Wang, Xiaohong, Warfsmann, Jens, Weissenbach, Jean, White, Doug D., White, Jim D., Wiley, Graham B., Wincker, Patrick, Xing, Yanbo, Yang, Limei, Yao, Ziyun, Ying, Fu, Zhai, Jixian, Zhou, Liping, Zuber, Antoine, Dénarié, Jean, Dixon, Richard A., May, Gregory D., Schwartz, David C., Rogers, Jane, Quétier, Francis, Town, Christopher D., and Roe, Bruce A.

Published
2011
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32. Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly

Author

Nieberding, Caroline M., primary, Beldade, Patrícia, additional, Baumlé, Véronique, additional, Martin, Gilles San, additional, Arun, Alok, additional, Lognay, Georges, additional, Montagné, Nicolas, additional, Bastin-Héline, Lucie, additional, Jacquin-Joly, Emmanuelle, additional, Noirot, Céline, additional, Klopp, Christophe, additional, and Visser, Bertanne, additional

Published
2020
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34. 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

35. Mosaic evolution of molecular pathways for sex pheromone communication in a butterfly

Author

UCL - SST/ELI/ELIB - Biodiversity, Nieberding, Caroline M., Beldade,Patricia, Baumlé, Véronique, San Martin, Gilles, Arun, Alok, Lognay, Georges, Montagné, Nicolas, Bastin-Héline, Lucie, Jacquin-Joly, Emmanuelle, Noirot, Céline, Klopp, Christophe, Visser, Bertanne, UCL - SST/ELI/ELIB - Biodiversity, Nieberding, Caroline M., Beldade,Patricia, Baumlé, Véronique, San Martin, Gilles, Arun, Alok, Lognay, Georges, Montagné, Nicolas, Bastin-Héline, Lucie, Jacquin-Joly, Emmanuelle, Noirot, Céline, Klopp, Christophe, and Visser, Bertanne

Abstract

Unraveling theorigin of molecular pathways underlying the evolution of adaptive traits is essential forunderstandinghow new lineagesemerge, including the relative contribution ofconserved, ancestral traits, and newly evolved, derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal)that occurred~98million years ago. In moths, females typically emit pheromones to attract male mates, but in butterflies pheromonesand used by females for mate choice. The molecular bases of sex pheromone communication arewellunderstood in moths, but haveremained virtually unexplored in butterflies. We useda combination of transcriptomics, real time qPCR, and phylogenetics, to identify genes involved in different steps of sex pheromone communication in the butterflyBicyclus anynana. Our results show that the biosynthesis and reception of sex pheromonesrelies both on moth-specific gene families (reductases) and onmore ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana further appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulationof sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale analysis of the genetic pathways underlying sex pheromone communication in a butterfly.

Published
2020

36. NG6: Integrated next generation sequencing storage and processing environment

Author

Mariette Jérôme, Escudié Frédéric, Allias Nicolas, Salin Gérald, Noirot Céline, Thomas Sylvain, and Klopp Christophe

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

Abstract Background Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. Results We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. Conclusions NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data.

Published
2012
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37. RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

Author

Villar Emilie, Klopp Christophe, Noirot Céline, Novaes Evandro, Kirst Matias, Plomion Christophe, and Gion Jean-Marc

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

Abstract Background In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit. Results Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed. Conclusions For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study.

Published
2011
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38. Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool

Author

Klopp Christophe, Noirot Céline, and Jérôme Mariette

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background Roche 454 pyrosequencing platform is often considered the most versatile of the Next Generation Sequencing technology platforms, permitting the sequencing of large genomes, the analysis of variations or the study of transcriptomes. A recent reported bias leads to the production of multiple reads for a unique DNA fragment in a random manner within a run. This bias has a direct impact on the quality of the measurement of the representation of the fragments using the reads. Other cleaning steps are usually performed on the reads before assembly or alignment. Findings PyroCleaner is a software module intended to clean 454 pyrosequencing reads in order to ease the assembly process. This program is a free software and is distributed under the terms of the GNU General Public License as published by the Free Software Foundation. It implements several filters using criteria such as read duplication, length, complexity, base-pair quality and number of undetermined bases. It also permits to clean flowgram files (.sff) of paired-end sequences generating on one hand validated paired-ends file and the other hand single read file. Conclusions Read cleaning has always been an important step in sequence analysis. The pyrocleaner python module is a Swiss knife dedicated to 454 reads cleaning. It includes commonly used filters as well as specialised ones such as duplicated read removal and paired-end read verification.

Published
2011
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39. Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

Author

Léger Patrick, Cabane Cyril, Abadie Pierre, Derory Jérémy, Brendel Oliver, Murat Florent, Abrouk Michael, Salse Jérôme, Salin Franck, Frigerio Jean-Marc, Noirot Céline, Klopp Christophe, Léger Valérie, Le Provost Grégoire, Ueno Saneyoshi, Barré Aurélien, de Daruvar Antoine, Couloux Arnaud, Wincker Patrick, Reviron Marie-Pierre, Kremer Antoine, and Plomion Christophe

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

Abstract Background The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity. Results We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html. Conclusions This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.

Published
2010
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40. Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

Author

Leterrier Christine, Richard Sabine, Gourichon David, Noirot Céline, Klopp Christophe, Bouchez Olivier, Vignoles Florence, Feve Katia, Leroux Sophie, Beaumont Catherine, Minvielle Francis, Vignal Alain, and Pitel Frédérique

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background SNP (Single Nucleotide Polymorphism) discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism) for genomic DNA, and EST (Expressed Sequence Tag) for the transcribed fraction of the genome. Findings The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. Conclusions Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA.

Published
2010
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41. 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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48. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

Author

Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, Romby, Pascale, Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, and Romby, Pascale

Abstract

Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA‐K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE‐mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C−rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism

Published
2017

49. Genome-wide methylation analysis of heat-acclimated chicken

Author

Coustham, Vincent, Esquerre, Diane, Noirot, Céline, Plenecassagnes, Julien, Lejeune, Clara, David, Sarah-Anne, Crochet, Sabine, Loyau, Thomas, Zerjal, Tatiana, Leroux, Sophie, Salin, Gérald, Collin, Anne, Pitel, Frédérique, Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Génétique Animale et Biologie Intégrative (GABI), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
genome-wide, chicken, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], methylation, [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2015

Catalog

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