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35 results on '"Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)"'

1. Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium

Author

M. V. Dziuba, A. Paulus, L. Schramm, R. P. Awal, M. Pósfai, C. L. Monteil, S. Fouteau, R. Uebe, D. Schüler, University of Bayreuth, University of Pannonia, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), European Union’s Horizon 2020 research and innovation program (Grant No. 692637), and ANR-20-CE92-0050,ANCESMAG,Reconstruction des séquences ancestrales et expression fonctionnelle des protéines impliquées dans la biogenèse des magnétosomes bactériens(2020)

Subjects
[SDV]Life Sciences [q-bio], Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract

Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.

Published
2022
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2. Fourth industrial revolution concepts in the automotive sector: performativity, work and employment

Author

Tommaso Pardi, Institutions et Dynamiques Historiques de l'Économie et de la Société (IDHES), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), and Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Nanterre (UPN)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris 1 Panthéon-Sorbonne (UP1)

Subjects
Economics and Econometrics, Industry 4.0, media_common.quotation_subject, Automotive industry, 02 engineering and technology, [SHS]Humanities and Social Sciences, 0203 mechanical engineering, 0502 economics and business, Domaine 1 - Travail, Advanced manufacturing, Quality (business), Business and International Management, Lagging, Industrial Revolution, Productivity, Industrial organization, media_common, sociologie, 9. Industry and infrastructure, business.industry, 05 social sciences, 020302 automobile design & engineering, Domaine 2 - Savoirs, General Business, Management and Accounting, 8. Economic growth, Digital manufacturing, business, General Economics, Econometrics and Finance, 050203 business & management
Abstract

International audience; In order to assess the possibility for a digital manufacturing revolution to take place in the automotive sector, the article reviews the historical evolution of automotive manufacturing technologies and organisations and analyses the impact on “fourth industrial revolution” concepts on their current transformations, taking into account in particular their consequences for employment and work. It shows that previous attempts of automating final assembly have failed because human based teamwork organizations have proved more flexible and efficient in dealing with complex assembly processes. It also highlights that the two main reasons behind these attempts in the past are not present anymore: important gaps in productivity and quality between leading and lagging firms; and shortages of skilled and unskilled manpower willing to work in automotive factories. The scope for a digital manufacturing revolution taking place in the automotive sector appears therefore limited. The analysis of the impact on automotive manufacturing of the three main “fourth industrial revolution” concepts in Germany (Industrie 4.0) in the US (advanced manufacturing), and in China (Made in China 2025) supports more than it challenges this historical understanding of the future of manufacturing in the automotive sector. It dismisses the idea that a fourth industrial revolution is under way and that a radical disruptive break will take place in the coming years.

Published
2019
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3. Towards standards for human fecal sample processing in metagenomic studies

Author

Rajna Hercog, Paul W. O'Toole, Melanie Tramontano, Thomas Carton, Michael Blaut, Muriel Derrien, John Penders, Ruth Ann Luna, Karen P. Scott, Milena Popova, Jillian R.M. Brown, Volker Mai, Francisco Guarner, Adriana Alberti, Nicolas Pons, Anne Druesne, Kiran Raosaheb Patil, Bhagirath Singh, Delphine M. Saulnier, Kathleen Slezak, Georg Zeller, Joël Doré, Clémentine Mery, Jennifer C. Martin, Jana Junick, Masahira Hattori, Harry J. Flint, Eric Pelletier, Florence Levenez, Liping Zhao, James Versalovic, Ingeborg Klymiuk, Jens Roat Kultima, Matthew R. Hayward, Shinichi Sunagawa, Søren Persson, Hans G.H.J. Heilig, Ferris Elias Jung, S. Dusko Ehrlich, Patrick Veiga, Anne Salonen, Stéphanie Cools-Portier, Chaysavanh Manichanh, Laurie Bertrand, Willem M. de Vos, Luis Pedro Coelho, B. Brett Finlay, Michelle C. Daigneault, Paul I. Costea, Céline Orvain, Philippe Langella, Johan E. T. van Hylckama Vlieg, Marja Driessen, Erwin G. Zoetendal, Emma Allen-Vercoe, Peer Bork, Hidetoshi Morita, Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), European Community's Seventh Framework Programme via International Human Microbiome Standards [HEALTH-F4-2010-261376], Scottish Government Rural and Environmental Science and Analytical Services, EMBL, European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), MetaGénoPolis, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Med Microbiol, Infect Dis & Infect Prev, RS: CAPHRI - R4 - Health Inequities and Societal Participation, RS: NUTRIM - R2 - Liver and digestive health, and RS: NUTRIM - R2 - Gut-liver homeostasis

Subjects
Quality Control, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Sample (material), 030106 microbiology, Sample processing, Biomedical Engineering, bacterial-dna, Bioengineering, Chemical Fractionation, Biology, Microbiology, Applied Microbiology and Biotechnology, diversity, dna-extraction methods, Feces, 03 medical and health sciences, Human gut, Species Specificity, Microbiologie, human gut microbiota, Biological variation, Humans, Life Science, Microbiome, VLAG, disease, Bacteria, business.industry, Computational Biology, DNA, DNA extraction, Biotechnology, 030104 developmental biology, Cardiovascular and Metabolic Diseases, Metagenomics, Molecular Medicine, business
Abstract

International audience; Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.

Published
2017
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4. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination

Author

Corinne Blugeon, Damarys Loew, Moussa Benhamed, Christophe Bailly, Fredy Barneche, Clara Bourbousse, Nicole Chaumont, Martin Rougée, Sophie Lemoine, David Latrasse, Chris Bowler, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Anne-Sophie Fiorucci, Ammara Mohammad, Bérangère Lombard, Elodie Layat, Lorenzo Concia, Soon Kap Kim, David Stroebel, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement (LBD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement [Paris] (LBD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Curie [Paris], Agence Nationale pour la Recherche (ANR) [ANR-11-JSV2-003-01], Investissements d'Avenir program, ANR [ANR-10-LABX-54 MEMOLIFE, ANR-10-IDEX-0001-02 PSL], Universite Paris-Sud Doctoral School in Plant Sciences, Region Ile-de-France, Fondation pour la Recherche Medicale, 'Investissements d'Avenir' program [ANR-10-INBS-09], Fiorucci, Anne-Sophie, Bourbousse, Clara, Barneche, Fredy, Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement [IBPS] (LBD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), GenomiqueENS (Genomique ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Gestionnaire, HAL Sorbonne Université 5, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
lcsh:QH426-470, [SDV]Life Sciences [q-bio], Protein subunit, Saccharomyces cerevisiae, Arabidopsis, Histones, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Histone H2B, Monoubiquitination, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:QH301-705.5, Gene, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Research, Ubiquitination, biology.organism_classification, Arabidopsis/metabolism, Histone Methyltransferases/metabolism, Histones/metabolism, Cell biology, [SDV] Life Sciences [q-bio], lcsh:Genetics, lcsh:Biology (General), Histone methyltransferase, Histone Methyltransferases, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], H3K4me3, 030217 neurology & neurosurgery
Abstract

Background The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role. Results We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Conclusions Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis. Electronic supplementary material The online version of this article (10.1186/s13059-019-1705-4) contains supplementary material, which is available to authorized users.

Published
2019
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5. Gibberellins negatively regulate the development of Medicago truncatula root system

Author

Camille Fonouni-Farde, Abdelhafid Bendahmane, Florian Frugier, Carole Laffont, Anouck Diet, Ambre Miassod, Halima Morin, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Frugier, Florian

Subjects
0301 basic medicine, lcsh:Medicine, Root system, Plant Roots, lateral root, purl.org/becyt/ford/1 [https], chemistry.chemical_compound, 0302 clinical medicine, Arabidopsis thaliana, PLASTICITY, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Plant Proteins, GIBBERELLIN, 2. Zero hunger, Multidisciplinary, biology, food and beverages, organization, Medicago truncatula, Cell biology, Plant species, Gibberellin, CIENCIAS NATURALES Y EXACTAS, growth, Meristem, Article, Ciencias Biológicas, 03 medical and health sciences, Expansin, ROOT, ground tissue, apical meristem, cell-layers, auxin, paclobutrazol, scarecrow, inhibit, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, purl.org/becyt/ford/1.6 [https], Gibberellic acid, Ciencias de las Plantas, Botánica, lcsh:R, fungi, 15. Life on land, biology.organism_classification, Gibberellins, 030104 developmental biology, chemistry, lcsh:Q, DELLA, 030217 neurology & neurosurgery
Abstract

The root system displays a remarkable plasticity that enables plants to adapt to changing environmental conditions. This plasticity is tightly linked to the activity of root apical meristems (RAMs) and to the formation of lateral roots, both controlled by related hormonal crosstalks. In Arabidopsis thaliana, gibberellins (GAs) were shown to positively control RAM growth and the formation of lateral roots. However, we showed in Medicago truncatula that GAs negatively regulate root growth and RAM size as well as the number of lateral roots depending at least on the MtDELLA1 protein. By using confocal microscopy and molecular analyses, we showed that GAs primarily regulate RAM size by affecting cortical cell expansion and additionally negatively regulate a subset of cytokinin-induced root expansin encoding genes. Moreover, GAs reduce the number of cortical cell layers, resulting in the formation of both shorter and thinner roots. These results suggest contrasting effects of GA regulations on the root system architecture depending on plant species. Fil: Fonouni-farde, Camille Audrey. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Miassod, Ambre. Universite Paris Saclay; Francia Fil: Laffont, Carole. Universite Paris Saclay; Francia Fil: Morin, Halima. Universite Paris Saclay; Francia Fil: Bendahmane, Abdelhafid. Universite Paris Saclay; Francia Fil: Diet, Anouck. Universite Paris Saclay; Francia Fil: Frugier, Florian. Universite Paris Saclay; Francia

Published
2019
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6. Annotation of microsporidian genomes using transcriptional signals

Author

Ivan Wawrzyniak, Sébastien Terrat, Olivier Gonçalves, Nicolas Parisot, Pierre Peyret, Patrick Wincker, Corinne Biderre-Petit, Simone Duprat, Frédéric Delbac, Jean Weissenbach, Sébastien Rimour, Eric Dugat-Bony, Antoine Mahul, Gaelle Samson, Brigitte Chebance, Stéphanie Bornes, Jérémie Denonfoux, Eric Peyretaillade, Michael Katinka, Valérie Polonais, Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Agroécologie [Dijon], Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes ( LIMOS ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Sigma CLERMONT ( Sigma CLERMONT ) -Centre National de la Recherche Scientifique ( CNRS ), Génie Biologie, Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Genomic platform and R&D, GenoScreen, Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre Régional de Ressources Informatiques (CRRI), Clermont Université, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), IUT Génie Biologique, Laboratoire de Biologie, Université d'Auvergne (Clermont Ferrand 1) (UdA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure des Mines de St Etienne, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
Transcription, Genetic, genome annotation, MESH : Molecular Sequence Annotation, General Physics and Astronomy, MESH: Phosphotransferases, Genome, transcriptional signal, MESH : Protein Transport, MESH : Fungal Proteins, DNA, Fungal, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, Fungal protein, MESH: Conserved Sequence, Multidisciplinary, MESH: Genomics, 030302 biochemistry & molecular biology, Genomics, Genome project, Protein Transport, Molecular Sequence Annotation, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Genome, Fungal, MESH: Fungal Proteins, MESH : Phosphotransferases, Genome, Fungal, Transposable element, MESH: Protein Transport, Genes, Fungal, MESH: Molecular Sequence Annotation, MESH : Microsporidia, MESH : Open Reading Frames, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Fungal Proteins, Open Reading Frames, 03 medical and health sciences, MESH : Conserved Sequence, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Anncaliia algerae, parasitic diseases, Gene, 030304 developmental biology, bioinformatic, MESH: Transcription, Genetic, MESH : Genome, Fungal, Phosphotransferases, structural annotation, MESH : Genomics, fungi, MESH : Transcription, Genetic, General Chemistry, MESH: Open Reading Frames, MESH: Microsporidia, MESH: DNA, Fungal, microsporidia, MESH : Genes, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH : DNA, Fungal, MESH: Genes, Fungal
Abstract

EA GenoSol CT3; International audience; High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidian-host relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. Such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.

Published
2012
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7. Correction: Transcriptome of the synganglion in the tick Ixodes ricinus and evolution of the cys-loop ligand-gated ion channel family in ticks

Author

Claude Rispe, Caroline Hervet, Nathalie de la Cotte, Romain Daveu, Karine Labadie, Benjamin Noel, Jean-Marc Aury, Steeve Thany, Emiliane Taillebois, Alison Cartereau, Anaïs Le Mauf, Claude L. Charvet, Clément Auger, Elise Courtot, Cédric Neveu, Olivier Plantard, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Università degli Studi di Pavia = University of Pavia (UNIPV), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Infectiologie et Santé Publique (UMR ISP), and Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

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

International audience

Published
2022
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8. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

Author

Christopher D. Town, Chris J Pires, Vivek Krishnakumar, Chushin Koh, Ian Bancroft, John Nixon, Matthew G. Links, Jérémy Just, Jacqueline Batley, Sahana Manoli, Matthew N. Nelson, Annaliese S. Mason, Jonathan D. Moore, Harry Belcram, Guy C. Barker, Xiyin Wang, Sateesh Kagale, Peter Glen Walley, Terry Huebert, David Edwards, Andrew G. Sharpe, Haibao Tang, Shelby L. Bidwell, Stephen J. Robinson, Tricia Bender, Isobel A. P. Parkin, Graham J.W. King, Carling Clarke, Andrew H. Paterson, Boulos Chalhoub, Wayne E. Clarke, Chalhoub, Boulos, Saskatoon Research Center, Partenaires INRAE, National Research Council of Canada (NRC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Agriculture and Agri-Food [Ottawa] (AAFC), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université d'Évry-Val-d'Essonne (UEVE), Inst Genom, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], Div Biol Sci, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, University of Warwick, University of Western Australia, University of Georgia [USA], Southern Cross University (SCU), University of York, Canadian Canola Genome Sequencing Initiative, Genome Alberta, industry partners, Agricultural Flexibility Fund, US National Science Foundation 0638536, Australian Research Council LP0882095 LP0883462 LP110100200, Australian Genome Research Facility (AGRF), Queensland Cyber Infrastructure Foundation (QCIF), UK Biotechnology and Biological Sciences Research Council BBSRC BB/E017363/1, DEFRA IF0157 Vegetable Genetic Improvement Network (VeGIN), Agriculture and Agri-Food (AAFC), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), University of Warwick [Coventry], and The University of Western Australia (UWA)

Subjects
0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], brassica oleracea, 01 natural sciences, Genome, Epigenesis, Genetic, Transcriptome, transcriptomics, Gene Expression Regulation, Plant, polyploidy, 2. Zero hunger, Genetics, 0303 health sciences, DNA methylation, Brassica rapa, Chromosome Mapping, food and beverages, genome size, Brassica oleracea, Ploidy, Genome, Plant, hexaploidy, Molecular Sequence Data, gene dosage, Brassica, Biology, Evolution, Molecular, 03 medical and health sciences, Polyploid, chou, polyploïdie, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, SB, Gene, Genome size, plant leaf, 030304 developmental biology, Research, QK, Molecular Sequence Annotation, Sequence Analysis, DNA, gene mapping, 15. Life on land, Aneuploidy, biology.organism_classification, diploïde, gene expression, 010606 plant biology & botany
Abstract

International audience; Background : Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Results : We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/ Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event. Conclusions : Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.

Published
2014
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9. Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Author

Elena Kazamia, Shinya Sato, Fabio Rocha Jimenez Vieira, Patrick Wincker, Zoltán Füssy, Deepak Nanjappa, Jean-Marc Aury, Olivier Jaillon, David G. Mann, Miroslav Oborník, Sergio A. Muñoz-Gómez, Leila Tirichine, Adriana Zingone, Chris Bowler, Alaguraj Veluchamy, Richard G. Dorrell, Roland Heilig, Fukui Prefectural University [Fukui, Japon], Stazione Zoologica Anton Dohrn (SZN), Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de fonctionnalité et ingénierie de protéines (UFIP), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), University of South Bohemia, Dalhousie University [Halifax], Royal Botanic Garden [Edinburgh], Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), D.N. acknowledges a fellowship funded by the Stazione Zoologica Anton Dohrn (SZN) within the SZN-Open University Ph.D. program. R.G.D. was supported by a CNRS Momentum Fellowship and E.K. was supported by the Marie Curie Postdoctoral Fellowship IRONCOMM. Work in the Bowler lab is supported by the Investissements d’Avenir programmes PSL and MEMOLIFE: MEMO LIFE (ANR-10-LABX-54), and PSL*Research University (ANR-11-IDEX-0001-02)., ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Royal Botanic Garden Edinburgh, Institute of Agrifood Research and Technology (IRTA), Producció Animal, Aigües Marines i Continentals, Bodescot, Myriam, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, and INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID

Subjects
0106 biological sciences, 0301 basic medicine, Science, Lineage (evolution), [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, 01 natural sciences, Genome, Article, Evolution, Molecular, 03 medical and health sciences, Algae, Phylogenetics, Genus, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 14. Life underwater, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Phylogeny, Diatoms, Multidisciplinary, Ecology, biology, Phylogenetic tree, Gene Expression Profiling, fungi, biology.organism_classification, Biological Evolution, Rhodobacterales, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Diatom, Evolutionary biology, Medicine, Transcriptome, 010606 plant biology & botany
Abstract

Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.

Published
2020
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10. XszenFHal, a novel tryptophan 5-halogenase from Xenorhabdus szentirmaii

Author

Carine Vergne-Vaxelaire, Anne Zaparucha, Jean-Louis Petit, Véronique de Berardinis, Aurélie Fossey-Jouenne, Adrien Debard, Diane Erdmann, Jérémy Domergue, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), The authors gratefully acknowledge Dr. Eugenio P. Patallo (Institut für Biochemie, TU Dresden, 01062 Dresden, Germany) for sending a sample of 7‑chloro tryptophan. They would like to thank Olek Maciejak and Marie‑Jeanne Clément (SABNP, INSERM U 1204—Université d’Evry Val‑d’Essonne, Université Paris‑Saclay, France) for assistance in 1H and 13C NMR experiments, the Region Ile de France for financial support of the 600 MHz NMR spectrometer, Dr. Alain Perret, Christine Pelle and Peggy Sirvain for protein supply, Virginie Pellouin for technical support., and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
Stereochemistry, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Biophysics, 010402 general chemistry, medicine.disease_cause, 01 natural sciences, Applied Microbiology and Biotechnology, lcsh:Microbiology, Regioselectivity, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Indole test, Flavin-dependent halogenases, 010405 organic chemistry, Chemistry, Tryptophan, Symbiotic bacterium, Halogenation, 0104 chemical sciences, enzyme, Electrophilic halogenation, Biocatalysis, Original Article, Indole derivatives, Xenorhabdus szentirmaii
Abstract

Flavin-dependent halogenases (FHals) catalyse the halogenation of electron-rich substrates, mainly aromatics. Halogenated compounds have many applications, as pharmaceutical, agrochemicals or as starting materials for the synthesis of complex molecules. By exploring the sequenced bacterial diversity, we discovered and characterized XszenFHal, a novel FHal from Xenorhabdus szentirmaii, a symbiotic bacterium of entomopathogenic nematode. The substrate scope of XszenFHal was examined and revealed activities towards tryptophan, indole and indole derivatives, leading to the formation of the corresponding 5-chloro products. XszenFHal makes a valuable addition to the panel of flavin-dependent halogenases already discovered and enriches the potential for biotechnology applications by allowing access to 5-halogenated indole derivatives.

Published
2019
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11. Tnt1 retrotransposon as an efficient tool for development of an insertional mutant collection of Lotus japonicus

Author

Miglena Revalska, Kevin Magne, Irina Boycheva, Pascal Ratet, Mariana Radkova, Anelia Iantcheva, Grigor Zehirov, Valya Vassileva, AgroBioInstitute, Institute of Plant Physiology and Genetics, Tajik Academy of Sciences, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Ministry of Education and Science of Republic Bulgaria [Do 02-268], and Agence Nationale de la Recherche (ANR) Blanc International SVSE [6.2010.1]

Subjects
0106 biological sciences, 0301 basic medicine, Somatic embryogenesis, Agrobacterium, [SDV]Life Sciences [q-bio], Nicotiana tabacum, Lotus japonicus, Retrotransposon, Plant Science, 01 natural sciences, Insertional mutagenesis, 03 medical and health sciences, Tnt1 retrotransposon, Botany, Starter lines, Regeneration, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genetics, biology, fungi, food and beverages, biology.organism_classification, Medicago truncatula, Transformation (genetics), 030104 developmental biology, Embryogenesis, [SDE]Environmental Sciences, 010606 plant biology & botany, Biotechnology
Abstract

International audience; The Tnt1 retrotransposon of tobacco (Nicotiana tabacum) has proven to be a very efficient mutagen for the model legume Medicago truncatula ecotype 108 and cultivar Jemalong 2HA and for economically important plants, such as soybean and potato. In this study, the activity of Tnt1 in the model legume Lotus japonicus L. was tested. First, a new regeneration and transformation protocol was developed for L. japonicus that represents a new tool for legume mutagenesis and reverse genetics. Using this protocol, the Tnt1 retrotransposon was introduced into L. japonicus by Agrobacterium tumefaciens-mediated transformation, and primary transgenic lines, named starter lines, were constructed. In vitro regeneration via indirect somatic embryogenesis using starter lines harboring two to eight copies of the transgene resulted in new Tnt1 transposition events. The Tnt1 retrotransposon remained inactive during plant growth and in the T-1 progeny, indicating that it is well suited for insertional mutagenesis in L. japonicus.

Published
2016
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12. Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence

Author

Zhong-Yi Cheng, Yue Lu, Qiutao Xu, Yue Yu, Yu Zhao, Dao-Xiu Zhou, Yuan Liu, National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), ingjie PTM BioLab Co Ltd, Partenaires INRAE, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), National Natural Science Foundation of China [31730049], National Key Research and Development Program of China [2016YFD0100802], Huazhong Agricultural University Scientific & Technological Self-innovation Foundation [2016RC003], Fundamental Research Funds for the Central Universities [2662015PY228], Huazhong Agricultural University, and Zhou, Dao-Xiu

Subjects
0301 basic medicine, ossrt1, lcsh:QH426-470, [SDV]Life Sciences [q-bio], Lysine, promoters, p300, Histones, 03 medical and health sciences, Gene Expression Regulation, Plant, Stress, Physiological, Gene expression, Sirtuins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, propionylation, lcsh:QH301-705.5, Plant Proteins, 2. Zero hunger, Regulation of gene expression, biology, Acetylation, Oryza, gene-expression, metabolic-regulation, Chromatin, Cell biology, transcription, arabidopsis, lcsh:Genetics, 030104 developmental biology, Histone, lcsh:Biology (General), Sirtuin, biology.protein, Histone deacetylase, Protein Processing, Post-Translational
Abstract

International audience; Background: Histone lysine acylations by short-chain fatty acids are distinct from the widely studied histone lysine acetylation in chromatin, although both modifications are regulated by primary metabolism in mammalian cells. It remains unknown whether and how histone acylation and acetylation interact to regulate gene expression in plants that have distinct regulatory pathways of primary metabolism. Results: We identify 4 lysine butyrylation (Kbu) sites (H3K14, H4K12, H2BK42, and H2BK134) and 45 crotonylation (Kcr) sites on rice histones by mass spectrometry. Comparative analysis of genome-wide Kbu and Kcr and H3K9ac in combination with RNA sequencing reveals 25,306 genes marked by Kbu and Kcr in rice and more than 95% of H3K9ac-marked genes are marked by both. Kbu and Kcr are enriched at the 5' region of expressed genes. In rice under starvation and submergence, Kbu and Kcr appear to be less dynamic and display changes in different sets of genes compared to H3K9ac. Furthermore, Kbu seems to preferentially poise gene activation by external stresses, rather than internal circadian rhythm which has been shown to be tightly associated with H3K9ac. In addition, we show that rice sirtuin histone deacetylase (SRT2) is involved in the removal of Kcr. Conclusion: Kbu, Kcr, and H3K9ac redundantly mark a large number of active genes but display different responses to external and internal signals. Thus, the proportion of rice histone lysine acetylation and acylation is dynamically regulated by environmental and metabolic cues, which may represent an epigenetic mechanism to fine-tune gene expression for plant adaptation.

Published
2018
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13. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

Author

Jean-Yves Coppée, Bernd Jagla, Zoé Rouy, Hugo Varet, Didier Mazel, Claudine Médigue, Oihane Irazoki, Evelyne Krin, Stéphane Cruveiller, Sebastian Aguilar Pierlé, Odile Sismeiro, Susana Campoy, Marie-Agnès Dillies, Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Universitat Autònoma de Barcelona (UAB), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), This study was funded by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS-UMR3525), the French National Research Agency (ANR-2012-Blanc SVSE3-DynamINT), the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°ANR-10-LABX-62-IBEID), the Spanish the Ministerio de Economía y Competitividad (BIO2016–77011-R), Generalitat de Catalunya (2014SGR 572), and the European Union Seventh Framework Programme (FP7-HEALTH-2011-single-stage) 'Evolution and Transfer of Antibiotic Resistance' (EvoTAR). The Transcriptome and EpiGenome Platform is a member of the France Génomique consortium (ANR10-NBS-09-08)., ANR-12-BSV3-0015,DynamINT,Recombination des cassettes d'intégron: dynamique in vivo et in vitro(2012), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 282004,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,EVOTAR(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
NcRNA, 0301 basic medicine, SOS response, lcsh:QH426-470, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Mitomycin, genetic processes, 030106 microbiology, DNA repair, Biology, medicine.disease_cause, Regulon, Transcriptome, 03 medical and health sciences, SOS Response (Genetics), lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, medicine, SOS Response, Genetics, Vibrio cholerae, Gene, Gene Expression Profiling, Promoter, biochemical phenomena, metabolism, and nutrition, ncRNA, nrdB, nrdA, lcsh:Genetics, enzymes and coenzymes (carbohydrates), Phenotype, bacteria, Repressor lexA, Transcription Initiation Site, NrdB, 5' Untranslated Regions, NrdA, Research Article, Biotechnology
Abstract

Background The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. Results Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5’UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369–1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. Conclusions We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria. Electronic supplementary material The online version of this article (10.1186/s12864-018-4716-8) contains supplementary material, which is available to authorized users.

Published
2018
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14. Altered DNA methylation associated with an abnormal liver phenotype in a cattle model with a high incidence of perinatal pathologies

Author

Hélène Jammes, Hélène Kiefer, Audrey Prézelin, Mireille Ledevin, Luc Jouneau, Marie-Laure Martin-Magniette, Daniel Le Bourhis, Pascale Chavatte-Palmer, Christophe Richard, Thibaut Larcher, Jean-Paul Renard, Yvan Heyman, Delphine Rousseau-Ralliard, Sandrine Balzergue, Evelyne Campion, Prézelin, Audrey, Chavatte Palmer, Pascale, Heyman, Yvan, Richard, Christophe, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Physiopathologie Animale et bioThérapie du muscle et du système nerveux (PAnTher), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UE 1298 Unité Commune d'Expérimentation Animale, Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR-09-GENM-012-01), APIS- GENE (13000394) and INRA’s Animal Physiology and Livestock Systems Division (ACI PHASE 2010), LabEx Saclay Plant Sciences - SPS (ANR-10-LABX-0040-SPS), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)

Subjects
Male, 0301 basic medicine, bovin, méthylation de l'adn, Cloning, Organism, variabilité phénotypique, Cattle Diseases, Biology, Article, Epigenesis, Genetic, 03 medical and health sciences, épigénétique, Stress, Physiological, pathologie, Genotype, Biologie de la reproduction, animal modèle, période perinatale, Animals, Epigenetics, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Gene, 2. Zero hunger, Regulation of gene expression, Cloning, Genetics, Reproductive Biology, maladie hépatique, Multidisciplinary, Fatty Acids, Biologie du développement, 0402 animal and dairy science, Gene Expression Regulation, Developmental, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, 04 agricultural and veterinary sciences, DNA Methylation, Development Biology, 040201 dairy & animal science, Phenotype, 3. Good health, Disease Models, Animal, 030104 developmental biology, Liver, DNA methylation, Cattle, Female, Energy Metabolism, TCF7L2
Abstract

Daniel Le Bourhis, present adress: ALLICE, Nouzilly, France Sandrine Balzergue, present adress: IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV; International audience; Cloning enables the generation of both clinically normal and pathological individuals from the same donor cells, and may therefore be a DNA sequence-independent driver of phenotypic variability. We took advantage of cattle clones with identical genotypes but different developmental abilities to investigate the role of epigenetic factors in perinatal mortality, a complex trait with increasing prevalence in dairy cattle. We studied livers from pathological clones dying during the perinatal period, clinically normal adult clones with the same genotypes as perinatal clones and conventional age-matched controls. The livers from deceased perinatal clones displayed histological lesions, modifications to quantitative histomorphometric and metabolic parameters such as glycogen storage and fatty acid composition, and an absence of birth-induced maturation. In a genome-wide epigenetic analysis, we identified DNA methylation patterns underlying these phenotypic alterations and targeting genes relevant to liver metabolism, including the type 2 diabetes gene TCF7L2. The adult clones were devoid of major phenotypic and epigenetic abnormalities in the liver, ruling out the effects of genotype on the phenotype observed. These results thus provide the first demonstration of a genome-wide association between DNA methylation and perinatal mortality in cattle, and highlight epigenetics as a driving force for phenotypic variability in farmed animals.

Published
2016
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15. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

Author

Wafa Frigui, Fadel Sayes, Camille Locht, Gregory Salvignol, Varun Khanna, Eve Willery, Danielle Walker, Anne-Sophie Debrie, Philip Supply, Michael Marceau, Timothy P. Stinear, Alessandro Cascioferro, Roland Brosch, Sylvain Brisse, Michael A. Quail, Stephen D. Bentley, Michel Fabre, Sophie Mangenot, Laurence Fiette, Claudine Médigue, Stéphane Cruveiller, Carine Rouanet, Claude Leclerc, Alexandre Pawlik, Julien Tap, Torsten Seemann, Laleh Majlessi, Christiane Bouchier, Roxane Simeone, Laurence Ma, David Roche, Cecile Parmentier, Valérie Barbe, Mickael Orgeur, Julian Parkhill, Eva C. Boritsch, Alexis Criscuolo, Maria-Cristina Gutierrez, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris] (IP), Régulation Immunitaire et Vaccinologie, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Histopathologie humaine et Modèles animaux, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), HIA Percy, Mécanismes moléculaires de la pathogénie microbienne, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Wellcome Trust Sanger Institute [Cambridge], Génomique (Plate-Forme) - Genomics Platform, Victorian Bioinformatics Consortium [Clayton], Monash University [Clayton], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Mécanismes moléculaires de la pathogenèse bactérienne, Département Infection et Epidémiologie - Department of Infection and Epidemiology, University of Melbourne, The work was supported in part by the Institut Pasteur (PTR 314 and PTR 383), European Community's Framework Programme 7 grant 260872, Wellcome Trust grant 098051 and Genoscope collaborative grant 114., European Project: 260872,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MM4TB(2011), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)

Subjects
MESH: Sequence Analysis, DNA, MESH: Mycobacterium tuberculosis, Tuberculosis, MESH: Spleen, [SDV]Life Sciences [q-bio], MESH: Mice, Inbred BALB C, Virulence, Genomics, MESH: Virulence, MESH: Base Sequence, MESH: Genome, Bacterial, Genome, DNA sequencing, Mycobacterium tuberculosis, 03 medical and health sciences, Genetic variation, Genetics, medicine, MESH: Species Specificity, MESH: Animals, MESH: Lung, MESH: Mice, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, biology, 030306 microbiology, MESH: Adaptation, Biological, MESH: Genomics, MESH: Polymorphism, Single Nucleotide, biology.organism_classification, medicine.disease, MESH: Cluster Analysis, 3. Good health, MESH: Inverted Repeat Sequences, Mycobacterium
Abstract

International audience; Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5× coverage), 454/Roche (13-18× coverage) and/or Illumina DNA sequencing (45-105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.

Published
2013
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16. Survey of the green picoalga Bathycoccus genomes in the global ocean

Author

Yoann Seeleuthner, Patrick Wincker, Samuel Mondy, Jean-Marc Aury, Daniele Iudicone, Jade Leconte, Olivier Jaillon, Michael E. Sieracki, Thomas Vannier, Daniel Vaulot, Eric Pelletier, Colomban de Vargas, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), National Science Foundation [Arlington] (NSF), Stazione Zoologica Anton Dohrn (SZN), Diversité et Interactions au sein du Plancton Océanique (DIPO), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
0301 basic medicine, Oceans and Seas, 030106 microbiology, Sequence assembly, Genomics, comparative genomics, Genome, Article, 18S ribosomal RNA, Bathycoccus, 03 medical and health sciences, Chlorophyta, Phylogenetics, Surveys and Questionnaires, Microalgae, RNA, Ribosomal, 18S, Seawater, biogeography, metagenomics, 14. Life underwater, Phylogeny, Ecotype, Comparative genomics, Genetics, Multidisciplinary, biology, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Metagenomics, Phytoplankton, Metagenome
Abstract

Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.

Published
2016
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17. Water orientation and hydrogen-bond structure at the fluorite/water interface

Author

Marie-Pierre Gaigeot, Ellen H. G. Backus, Marialore Sulpizi, Mischa Bonn, Rémi Khatib, María-José Perez-Haro, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Max Planck Institute for Polymer Research, Max-Planck-Gesellschaft, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Johannes Gutenberg - Universität Mainz (JGU), and Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Materials science, Chemical physics, [SDV]Life Sciences [q-bio], FOS: Physical sciences, 02 engineering and technology, Electronic structure, Molecular dynamics, 010402 general chemistry, 01 natural sciences, Article, Spectral line, Ion, chemistry.chemical_compound, Adsorption, Physics - Chemical Physics, Surface charge, Dissolution, Chemical Physics (physics.chem-ph), Multidisciplinary, Hydrogen bond, 021001 nanoscience & nanotechnology, Surface spectroscopy, 0104 chemical sciences, Geochemistry, chemistry, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 0210 nano-technology, Fluoride
Abstract

Water in contact with mineral interfaces is important for a variety of different processes. Here, we present a combined theoretical/experimental study which provides a quantitative, molecular-level understanding of the ubiquitous and important CaF2/water interface. Our results show that, at low pH, the surface is positively charged, causing a substantial degree of water ordering. The surface charge originates primarily from the dissolution of fluoride ions, rather than from adsorption of protons to the surface. At high pH we observe the presence of Ca-OH species pointing into the water. These OH groups interact remarkably weakly with the surrounding water and are responsible for the “free OH” signature in the VSFG spectrum, which can be explained from local electronic structure effects. The quantification of the surface termination, near-surface ion distribution and water arrangement is enabled by a combination of advanced phase-resolved Vibrational Sum Frequency Generation spectra of CaF2/water interfaces and state-of-the-art ab initio molecular dynamics simulations which include electronic structure effects.

Published
2016
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18. Role of AGC kinases in plant growth and stress responses

Author

Heribert Hirt, Mohamed S Alyousif, Ana Victoria Garcia, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Coll Sci, Swansea University, ANR MAPK, EU ADYSARC, and Systems Biology SHIPREC

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Arabidopsis, medicine.disease_cause, 01 natural sciences, Phosphatidylinositol 3-Kinases, DISEASE RESISTANCE, AGC kinases, FLAGELLIN PERCEPTION, Genetics, 0303 health sciences, Mutation, Kinase, TOR, Plants, Cell biology, PDK1, Mitogen-activated protein kinase, Molecular Medicine, S6 KINASE, Cell death, Programmed cell death, MAP Kinase Signaling System, FUNGUS PIRIFORMOSPORA-INDICA, Morphogenesis, Plant Development, Plant Immunity, Protein Serine-Threonine Kinases, Biology, 3-Phosphoinositide-Dependent Protein Kinases, 03 medical and health sciences, Cellular and Molecular Neuroscience, Plant immunity, Stress, Physiological, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Protein kinase A, Molecular Biology, 030304 developmental biology, Pharmacology, Arabidopsis Proteins, Cell growth, Basidiomycota, Cell Biology, PROTEIN-KINASE, stomatognathic diseases, CELL-DEATH, ARABIDOPSIS-THALIANA, INNATE IMMUNITY, biology.protein, PSEUDOMONAS-SYRINGAE, Protein Kinases, AUXIN TRANSPORT, 010606 plant biology & botany
Abstract

International audience; AGC kinases are important regulators of cell growth, metabolism, division, and survival in mammalian systems. Mutation or deregulation of members of this family of protein kinases contribute to the pathogenesis of many human diseases, including cancer and diabetes. Although AGC kinases are conserved in the plant kingdom, little is known about their molecular functions and targets. Some of the best-studied plant AGC kinases mediate auxin signaling and are thereby involved in the regulation of growth and morphogenesis. Furthermore, certain members are regulated by lipid-derived signals via the 3-phosphoinositide-dependent kinase 1 (PDK1) and the kinase target of rapamycin (TOR), similar to its animal counterparts. In this review, we discuss recent findings on plant AGC kinases that unravel important roles in the regulation of plant growth, immunity and cell death, and connections to stress-induced mitogen-activated protein kinase signaling cascades.

Published
2012
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19. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Author

Gaëtan Droc, Adriana Alberti, Philippe Francois, Rémy Habas, Patrick Wincker, Jaroslav Dolezel, Mouna Jeridi, Cyril Jourda, E. Hribova, Thomas Wicker, Kamel Jabbari, Julie Leclercq, Cees Waalwijk, Olivier Panaud, Benjamin Noel, Marlã̈ne Souquet, Manuel Ruiz, Didier Mbéguié-A-Mbéguié, Margot Correa, Nicolas Roux, Saravanaraj Ayyampalayam, Ronan Rivallan, Spencer Brown, Françoise Carreel, Maria Bernard, Andrzej Kilian, Jose Barbosa, Olivier Jaillon, Olivier Garsmeur, Jean-Marc Aury, Ange-Marie Risterucci, Julie Poulain, Karine Labadie, Xavier Argout, Steeve Joseph, Pat Heslop-Harrison, Jean-Christophe Glaszmann, Ana Maria Rocha de Almeida, Mathieu Rouard, Jean Weissenbach, Stéphanie Bocs, Juliette Lengellé, Nabila Yahiaoui, Eric Lyons, Anne Dievart, Corinne Da Silva, Marguerite Rodier-Goud, Dheema Burthia, Céline Cardi, Michael Freeling, Angélique D'Hont, Claire Poiron, Valentin Guignon, Matthieu Chabannes, Frédéric Bakry, Christophe Jenny, Franc-Christophe Baurens, Michael R. McKain, Miguel A. Dita, Francis Quetier, Diane Burgess, Jim Leebens-Mack, Gert H. J. Kema, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Optique Atmosphérique - UMR 8518 (LOA), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Wageningen University and Research Centre [Wageningen] (WUR), University of Zurich, and D'Hont, Angélique

Subjects
MESH: Genome, Plant, 0106 biological sciences, Phylogénie, Lineage (evolution), Plant genetics, Évolution, 580 Plants (Botany), Haploidy, resource, in-situ hybridization, Musa acuminata, 01 natural sciences, F30 - Génétique et amélioration des plantes, MESH: Genotype, sequence count data, 10126 Department of Plant and Microbial Biology, Gene Duplication, Musa balbisiana, dna sequences, MESH: Genes, Plant, maximum likelihood, MESH: Phylogeny, Conserved Sequence, Phylogeny, MESH: Evolution, Molecular, 2. Zero hunger, 0303 health sciences, MESH: Conserved Sequence, Multidisciplinary, MESH: Gene Duplication, food and beverages, F70 - Taxonomie végétale et phytogéographie, MESH: Haploidy, MESH: DNA Transposable Elements, Génotype, Genome, Plant, dna-sequences, Séquence nucléotidique, diversification, Poales, Genotype, Molecular Sequence Data, Biology, Poaceae, Genes, Plant, differential expression, Evolution, Molecular, Zingiberales, Biointeractions and Plant Health, 03 medical and health sciences, MESH: Musa, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gene, Domestication, 030304 developmental biology, 1000 Multidisciplinary, Génome, MESH: Molecular Sequence Data, Bioint Moleculair Phytopathology, rice, Musa, 15. Life on land, biology.organism_classification, Arecales, DNA Transposable Elements, identification, maximum-likelihood, in situ hybridization, 010606 plant biology & botany
Abstract

International audience; Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.

Published
2012
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20. Genome sequencing and analysis of the model grass Brachypodium distachyon

Author

Vogel, John P, Garvin, David F, Mockler, Todd C, Schmutz, Jeremy, Rokhsar, Dan, Bevan, Michael W, Barry, Kerrie, Lucas, Susan, Harmon-Smith, Miranda, Lail, Kathleen, Tice, Hope, Schmutz Leader, Jeremy, Grimwood, Jane, McKenzie, Neil, Huo, Naxin, Gu, Yong Q, Lazo, Gerard R, Anderson, Olin D, Vogel Leader, John P, You, Frank M, Luo, Ming-Cheng, Dvorak, Jan, Wright, Jonathan, Febrer, Melanie, Idziak, Dominika, Hasterok, Robert, Lindquist, Erika, Wang, Mei, Fox, Samuel E, Priest, Henry D, Filichkin, Sergei A, Givan, Scott A, Bryant, Douglas W, Chang, Jeff H, Mockler Leader, Todd C, Wu, Haiyan, Wu, Wei, Hsia, An-Ping, Schnable, Patrick S, Kalyanaraman, Anantharaman, Barbazuk, Brad, Michael, Todd P, Hazen, Samuel P, Bragg, Jennifer N, Laudencia-Chingcuanco, Debbie, Weng, Yiqun, Haberer, Georg, Spannagl, Manuel, Mayer Leader, Klaus, Rattei, Thomas, Mitros, Therese, Lee, Sang-Jik, Rose, Jocelyn K. C, Mueller, Lukas A, York, Thomas L, Wicker Leader, Thomas, Buchmann, Jan P, Tanskanen, Jaakko, Schulman Leader, Alan H, Gundlach, Heidrun, Bevan, Michael, Costa de Oliveira, Antonio, da C. Maia, Luciano, Belknap, William, Jiang, Ning, Lai, Jinsheng, Zhu, Liucun, Ma, Jianxin, Sun, Cheng, Pritham, Ellen, Salse Leader, Jerome, Murat, Florent, Abrouk, Michael, Mayer, Klaus, Bruggmann, Remy, Messing, Joachim, Fahlgren, Noah, Sullivan, Christopher M, Carrington, James C, Chapman, Elisabeth J, May, Greg D, Zhai, Jixian, Ganssmann, Matthias, Guna Ranjan Gurazada, Sai, German, Marcelo, Meyers, Blake C, Green Leader, Pamela J, Tyler, Ludmila, Wu, Jiajie, Thomson, James, Chen, Shan, Scheller, Henrik V, Harholt, Jesper, Ulvskov, Peter, Kimbrel, Jeffrey A, Bartley, Laura E, Cao, Peijian, Jung, Ki-Hong, Sharma, Manoj K, Vega-Sanchez, Miguel, Ronald, Pamela, Dardick, Christopher D, De Bodt, Stefanie, Verelst, Wim, Inzé, Dirk, Heese, Maren, Schnittger, Arp, Yang, Xiaohan, Kalluri, Udaya C, Tuskan, Gerald A, Hua, Zhihua, Vierstra, Richard D, Cui, Yu, Ouyang, Shuhong, Sun, Qixin, Liu, Zhiyong, Yilmaz, Alper, Grotewold, Erich, Sibout, Richard, Hematy, Kian, Mouille, Gregory, Höfte, Herman, Michael, Todd, Pelloux, Jérome, O’Connor, Devin, Schnable, James, Rowe, Scott, Harmon, Frank, Cass, Cynthia L, Sedbrook, John C, Byrne, Mary E, Walsh, Sean, Higgins, Janet, Li, Pinghua, Brutnell, Thomas, Unver, Turgay, Budak, Hikmet, Belcram, Harry, Charles, Mathieu, Chalhoub, Boulos, Baxter, Ivan, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), US Department of Energy Joint Genome Institute, BBSRC, EU, GABI Barlex, and Oregon State Agricultural Research Foundation

Subjects
Crops, Agricultural, 0106 biological sciences, Genome evolution, Transcription, Genetic, Molecular Sequence Data, POOIDEAE, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Genes, Plant, Poaceae, Synteny, 01 natural sciences, Genome, Chromosomes, Plant, EHRHARTOIDEAE, Evolution, Molecular, 03 medical and health sciences, Botany, Triticeae, Sorghum, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Multidisciplinary, biology, CULTURE VIVRIERE, Life Sciences, food and beverages, Oryza, Sequence Analysis, DNA, biology.organism_classification, ENERGIE RENOUVELABLE, Pooideae, RNA, Plant, Panicoideae, Evolutionary biology, PANICOIDEAE, DNA Transposable Elements, Brachypodium, Brachypodium distachyon, Gene Fusion, Genome, Plant, BRACHYPODIUM DISTACHYON, 010606 plant biology & botany
Abstract

Principal investigators John P. Vogel1, David F. Garvin2, Todd C. Mockler3, Jeremy Schmutz4, Dan Rokhsar5,6, Michael W. Bevan7; DNA sequencing and assembly Kerrie Barry5, Susan Lucas5, Miranda Harmon-Smith5, Kathleen Lail5, Hope Tice5, Jeremy Schmutz4 (Leader), Jane Grimwood4, Neil McKenzie7, Michael W. Bevan7; Pseudomolecule assembly and BACend sequencing Naxin Huo1, Yong Q.Gu1,Gerard R. Lazo1, Olin D.Anderson1, John P. Vogel1 (Leader), Frank M. You8,Ming-Cheng Luo8, Jan Dvorak8, Jonathan Wright7, Melanie Febrer7, Michael W. Bevan7, Dominika Idziak9, Robert Hasterok9, David F. Garvin2; Transcriptome sequencing and analysis Erika Lindquist5, Mei Wang5, Samuel E. Fox3, Henry D. Priest3, Sergei A. Filichkin3, Scott A. Givan3, Douglas W. Bryant3, Jeff H.Chang3, Todd C.Mockler3 (Leader), Haiyan Wu10,24, Wei Wu10, An-Ping Hsia10, Patrick S. Schnable10,24, Anantharaman Kalyanaraman11, Brad Barbazuk12, Todd P.Michael13, Samuel P.Hazen14, Jennifer N. Bragg1, Debbie Laudencia-Chingcuanco1, John P. Vogel1, David F. Garvin2, Yiqun Weng15, Neil McKenzie7, Michael W. Bevan7; Gene analysis and annotation Georg Haberer16, Manuel Spannagl16, Klaus Mayer16 (Leader), Thomas Rattei17, Therese Mitros6, Dan Rokhsar6, Sang-Jik Lee18, Jocelyn K.C. Rose18, Lukas A. Mueller19, Thomas L. York19; Repeats analysis Thomas Wicker20 (Leader), Jan P. Buchmann20, Jaakko Tanskanen21, Alan H. Schulman21 (Leader), Heidrun Gundlach16, Jonathan Wright7, Michael Bevan7, Antonio Costa de Oliveira22, Luciano da C. Maia22, William Belknap1, Yong Q. Gu1, Ning Jiang23, Jinsheng Lai24, Liucun Zhu25, JianxinMa25, Cheng Sun26, Ellen Pritham26; Comparative genomics Jerome Salse27 (Leader), Florent Murat27, Michael Abrouk27, Georg Haberer16, Manuel Spannagl16, Klaus Mayer16, Remy Bruggmann13, Joachim Messing13, Frank M. You8, Ming-Cheng Luo8, Jan Dvorak8; Small RNA analysis Noah Fahlgren3, Samuel E. Fox3, Christopher M. Sullivan3, Todd C. Mockler3, James C. Carrington3, Elisabeth J. Chapman3,28, Greg D.May29, Jixian Zhai30, Matthias Ganssmann30, Sai Guna Ranjan Gurazada30, Marcelo German30, Blake C. Meyers30, Pamela J. Green30 (Leader); Manual annotation and gene family analysis Jennifer N. Bragg1, Ludmila Tyler1,6, Jiajie Wu1,8, Yong Q. Gu1, Gerard R. Lazo1, Debbie Laudencia-Chingcuanco1, James Thomson1, John P. Vogel1 (Leader), Samuel P. Hazen14, Shan Chen14, Henrik V. Scheller31, Jesper Harholt32, Peter Ulvskov32, Samuel E. Fox3, Sergei A. Filichkin3, Noah Fahlgren3, Jeffrey A. Kimbrel3, Jeff H. Chang3, Christopher M. Sullivan3, Elisabeth J. Chapman3,27, James C. Carrington3, Todd C. Mockler3, Laura E. Bartley8,31, Peijian Cao8,31, Ki-Hong Jung8,31, Manoj K Sharma8,31, Miguel Vega-Sanchez8,31, Pamela Ronald8,31, Christopher D.Dardick33, Stefanie De Bodt34,Wim Verelst34, Dirk Inze34, Maren Heese35, Arp Schnittger35, Xiaohan Yang36, Udaya C. Kalluri36, Gerald A. Tuskan36, Zhihua Hua37, Richard D. Vierstra37, David F. Garvin3, Yu Cui24, Shuhong Ouyang24, Qixin Sun24, Zhiyong Liu24, Alper Yilmaz38, Erich Grotewold38, Richard Sibout39, Kian Hematy39, Gregory Mouille39, Herman Höfte39, Todd Michael13, Jérome Pelloux40, Devin O'Connor41, James Schnable41, Scott Rowe41, Frank Harmon41, Cynthia L. Cass42, John C. Sedbrook42, Mary E. Byrne7, Sean Walsh7, Janet Higgins7, Michael Bevan7, Pinghua Li19, Thomas Brutnell19, Turgay Unver43,Hikmet Budak43, Harry Belcram44, Mathieu Charles44, Boulos Chalhoub44, Ivan Baxter45 1 USDA-ARS Western Regional Research Center, Albany, California 94710, USA. 2 USDA-ARS Plant Science Research Unit and University of Minnesota, St Paul, Minnesota 55108, USA. 3 Oregon State University, Corvallis, Oregon 97331-4501, USA. 4 HudsonAlpha Institute, Huntsville, Alabama 35806, USA. 5 US DOE Joint Genome Institute, Walnut Creek, California 94598, USA. 6 University of California Berkeley, Berkeley, California 94720, USA. 7 John Innes Centre, Norwich NR4 7UJ, UK. 8 University of California Davis, Davis, California 95616, USA. 9 University of Silesia, 40-032 Katowice, Poland. 10 Iowa State University, Ames, Iowa 50011, USA. 11 Washington State University, Pullman, Washington 99163, USA. 12 University of Florida, Gainsville, Florida 32611, USA. 13 Rutgers University, Piscataway, New Jersey 08855-0759, USA. 14 University of Massachusetts, Amherst, Massachusetts 01003-9292, USA. 15 USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706, USA. 16 Helmholtz Zentrum München, D-85764 Neuherberg, Germany. 17 Technical University München, 80333 München, Germany. 18 Cornell University, Ithaca, New York 14853, USA. 19 Boyce Thompson Institute for Plant Research, Ithaca, New York 14853-1801, USA. 20 University of Zurich, 8008 Zurich, Switzerland. 21 MTT Agrifood Research and University of Helsinki, FIN-00014 Helsinki, Finland. 22 Federal University of Pelotas, Pelotas, 96001-970, RS, Brazil. 23 Michigan State University, East Lansing, Michigan 48824, USA. 24 China Agricultural University, Beijing 10094, China. 25 Purdue University, West Lafayette, Indiana 47907, USA. 26 The University of Texas, Arlington, Arlington, Texas 76019, USA. 27 Institut National de la Recherche Agronomique UMR 1095, 63100 Clermont-Ferrand, France. 28 University of California San Diego, La Jolla, California 92093, USA. 29 National Centre for Genome Resources, Santa Fe, New Mexico 87505, USA. 30 University of Delaware, Newark, Delaware 19716, USA. 31 Joint Bioenergy Institute, Emeryville, California 94720, USA. 32 University of Copenhagen, Frederiksberg DK-1871, Denmark. 33 USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia 25430, USA. 34 VIB Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium. 35 Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg 67084, France. 36 BioEnergy Science Center and Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, USA. 37 University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. 38 The Ohio State University, Columbus, Ohio 43210, USA. 39 Institut Jean-Pierre Bourgin, UMR1318, Institut National de la Recherche Agronomique, 78026 Versailles cedex, France. 40 Université de Picardie, Amiens 80039, France. 41 Plant Gene Expression Center, University of California Berkeley, Albany, California 94710, USA. 42 Illinois State University and DOE Great Lakes Bioenergy Research Center, Normal, Illinois 61790, USA. 43 Sabanci University, Istanbul 34956, Turkey. 44 Unité de Recherche en Génomique Végétale: URGV (INRA-CNRS-UEVE), Evry 91057, France. 45 USDA-ARS/Donald Danforth Plant Science Center, St Louis, Missouri 63130, USA.; Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

Published
2010
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21. On truthfulness and approximation for scheduling selfish tasks

Author

Eric Angel, Fanny Pascual, Alex-Ariel Tchetgnia, Evripidis Bampis, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Recherche Opérationnelle (RO), Laboratoire d'Informatique de Paris 6 (LIP6), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)

Subjects
Discrete mathematics, Mechanism design, Mathematical optimization, 021103 operations research, Job shop scheduling, Scheduling, Computer science, 0211 other engineering and technologies, General Engineering, Approximation algorithm, 0102 computer and information sciences, 02 engineering and technology, Management Science and Operations Research, 01 natural sciences, Approximation algorithms, Scheduling (computing), 010201 computation theory & mathematics, Artificial Intelligence, [INFO]Computer Science [cs], Truthfulness, Game theory, Software
Abstract

International audience; We consider the problem of designing truthful mechanisms for scheduling n tasks on a set of m parallel related machines in order to minimize the makespan. In what follows, we consider that each task is owned by a selfish agent. This is a variant of the KP-model introduced by Koutsoupias and Papadimitriou (Proc. of STACS 1999, pp. 404-413, 1999) (and of the CKN-model of Christodoulou et al. in Proc. of ICALP 2004, pp. 345-357, 2004) in which the agents cannot choose the machine on which their tasks will be executed. This is done by a centralized authority, the scheduler. However, the agents may manipulate the scheduler by providing false information regarding the length of their tasks. We introduce the notion of increasing algorithm and a simple reduction that transforms any increasing algorithm into a truthful one. Furthermore, we show that some of the classical scheduling algorithms are indeed increasing: the LPT algorithm, the PTAS of Graham (SIAM J. Appl. Math. 17(2):416-429, 1969) in the case of two machines, as well as a simple PTAS for the case of m machines, with m a fixed constant. Our results yield a randomized r(1+ε)-approximation algorithm where r is the ratio between the largest and the smallest speed of the related machines. Furthermore, by combining our approach with the classical result of Shmoys et al. (SIAM J. Comput. 24(6):1313-1331, 1995), we obtain a randomized 2r(1+ε)-competitive algorithm. It has to be noticed that these results are obtained without payments, unlike most of the existing works in the field of Mechanism Design. Finally, we show that if payments are allowed then our approach gives a (1+ε)-algorithm for the off-line case with related machines.

Published
2009
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22. Arabidopsis MCM2 is responsible for reduction in cell division induced by loss of function of the alpha subunit of GTP-binding protein

Author

Dong-mei Yin, Ke Liang, Di-An Ni, Cécile Raynaud, Su-fen Chen, Shanghai Institute of Technology (SIT), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Innovation Program of Shanghai Municipal Education Commission [13YZ122, 14YZ141], Science Foundation of the Shanghai Municipal Science, and Technology Commission [13ZR1441300], and Shanghai Institute of Technology Scientific Research Foundation for Introduced Talent [YJ2012-26]

Subjects
Cell division, biology, Physiology, [SDV]Life Sciences [q-bio], fungi, Mutant, Heterotrimeric GTP-binding proteins (G proteins), food and beverages, Minichromosome maintenance (MCM), Plant Science, biology.organism_classification, Molecular biology, Hypocotyl, SCN3A, Minichromosome maintenance, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Agronomy and Crop Science, Gene, G alpha subunit
Abstract

International audience; Previous studies have reported reduction in cell division in seedlings of plants harbouring mutations in the alpha subunit of GTP-binding protein (gpa1). Notably, gpa1 mutants display reduced numbers of hypocotyl cells. Here we show that relative transcript level of the Arabidopsis minichromosome maintenance gene 2 (AtMCM2) is lower in gpa1 mutants than in wild-type Arabidopsis. Furthermore, expression of the AtMCM2 gene under the AtRb promoter restored hypocotyl cell number in gpa1 mutants. These results indicate that reduction in AtMCM2 gene is responsible for the reduction in hypocotyl cell division induced by loss of function of the alpha subunit of GTP-binding protein.

Published
2015
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23. A spectroscopic and voltammetric study of the pH-dependent Cu(II) coordination to the peptide GGGTH: relevance to the fifth Cu(II) site in the prion protein

Author

Florence Gonnet, Lorenzo Spadini, Pierre Dorlet, Jean-Jacques Girerd, Laurent Charlet, Christelle Hureau, Elodie Anxolabéhère-Mallart, Laboratoire de Géophysique Interne et Tectonophysique (LGIT), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Laboratoire Central des Ponts et Chaussées (LCPC)-Institut des Sciences de la Terre (ISTerre), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut national des sciences de l'Univers (INSU - CNRS)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-PRES Université de Grenoble-Institut de recherche pour le développement [IRD] : UR219-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Analyse et environnement (LAE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Central des Ponts et Chaussées (LCPC)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Central des Ponts et Chaussées (LCPC)-Centre National de la Recherche Scientifique (CNRS), and Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Spectrometry, Mass, Electrospray Ionization, Prions, Electrospray ionization, Potentiometric titration, Inorganic chemistry, Peptide, 010402 general chemistry, Electrochemistry, 01 natural sciences, Biochemistry, Pentapeptide repeat, law.invention, Inorganic Chemistry, law, Electrospray ionization mass spectrometry, Prion peptide, Spectroscopy, Electron paramagnetic resonance, Cu(II) complexes, chemistry.chemical_classification, 010405 organic chemistry, Chemistry, Electron Spin Resonance Spectroscopy, Hydrogen-Ion Concentration, 0104 chemical sciences, Crystallography, Potentiometry, Spectrophotometry, Ultraviolet, Cyclic voltammetry, Oligopeptides, Copper, Electron paramagnetic resonance spectroscopy
Abstract

The GGGTH sequence has been proposed to be the minimal sequence involved in the binding of a fifth Cu(II) ion in addition to the octarepeat region of the prion protein (PrP) which binds four Cu(II) ions. Coordination of Cu(II) by the N- and C-protected Ac-GGGTH-NH(2) pentapeptide (P(5)) was investigated by using potentiometric titration, electrospray ionization mass spectrometry, UV-vis spectroscopy, electron paramagnetic resonance (EPR) spectroscopy and cyclic voltammetry experiments. Four different Cu(II) complexes were identified and characterized as a function of pH. The Cu(II) binding mode switches from NO(3) to N(4) for pH values ranging from 6.0 to 10.0. Quasi-reversible reduction of the [Cu(II)(P(5))H(-2)] complex formed at pH 6.7 occurs at E (1/2)=0.04 V versus Ag/AgCl, whereas reversible oxidation of the [Cu(II)(P(5))H(-3)](-) complex formed at pH 10.0 occurs at E (1/2)=0.66 V versus Ag/AgCl. Comparison of our EPR data with those of the rSHaPrP(90-231) (Burns et al. in Biochemistry 42:6794-6803, 2003) strongly suggests an N(3)O binding mode at physiological pH for the fifth Cu(II) site in the protein.

Published
2006
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24. Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library

Author

C. L. Barker, Mark R. Thomas, T. Donald, A. Bouquet, Ian B. Dry, Milind B. Ratnaparkhe, J. Pauquet, Anne-Françoise Adam-Blondon, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University [Blacksburg], Biologie du développement des espèces pérennes cultivées (UMR BEPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Unité de recherche en génomique végétale (URGV), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Chromosomes, Artificial, Bacterial, Positional cloning, Locus (genetics), Biology, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Ascomycota, Gene mapping, Genetics, Gene, Plant Diseases, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Bacterial artificial chromosome, Contig, Chromosome Mapping, food and beverages, Sequence Analysis, DNA, General Medicine, Immunity, Innate, Vitaceae, Genetic marker, Agronomy and Crop Science, Powdery mildew, Microsatellite Repeats, 010606 plant biology & botany, Biotechnology
Abstract

International audience; Resistance to grapevine powdery mildew is controlled by Run1, a single dominant gene present in the wild grapevine species, Muscadinia rotundifolia, but absent from the cultivated species, Vitis vinifera. Run1 has been introgressed into V. vinifera using a pseudobackcross strategy, and genetic markers have previously been identified that are linked to the resistance locus. Here we describe the construction of comprehensive genetic and physical maps spanning the resistance locus that will enable future positional cloning of the resistance gene. Physical mapping was performed using a bacterial artificial chromosome (BAC) library constructed using genomic DNA extracted from a resistant V. vinifera individual carrying Run1 within an introgression. BAC contig assembly has enabled 20 new genetic markers to be identified that are closely linked to Run1, and the position of the resistance locus has been refined, locating the gene between the simple sequence repeat (SSR) marker, VMC4f3.1, and the BAC end sequence- derived marker, CB292.294. This region contains two multigene families of resistance gene analogues (RGA). A comparison of physical and genetic mapping data indicates that recombination is severely repressed in the vicinity of Run1, possibly due to divergent sequence contained within the introgressed fragment from M. rotundifolia that carries the Run1 gene.

Published
2005
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25. Profiling histone modification patterns in plants using genomic tiling microarrays

Author

Anne-Valérie Gendrel, Robert A. Martienssen, Vincent Colot, Zachary B. Lippman, Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Genetics, Chromatin Immunoprecipitation, [SDV]Life Sciences [q-bio], Arabidopsis, Acetylation, Cell Biology, Biology, Methylation, Biochemistry, Cell biology, [SDV] Life Sciences [q-bio], Histones, Histone H3, Histone H1, Histone methyltransferase, Histone H2A, Histone methylation, Histone code, Nucleosome, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Biotechnology, Epigenomics
Abstract

In eukaryotes, the processes of transcription, replication and homologous recombination occur in the context of chromatin. Although tightly packed, this structure is highly dynamic, being modified through the action of many enzymatic activities that reorganize nucleosomes; covalently modify histones through acetylation, phosphorylation, methylation and so on; exchange histones with variants; and in many eukaryotes, including plants and mammals, methylate DNA residues(1). Transcriptional activity is usually associated with hyperacetylation of histones tails as well as with di- or trimethylation of Lys4 in histone H3. Conversely, silent chromatin typically correlates with histone hypoacetylation and di- or trimethylation of histone H3 Lys9 (refs. 2,3). Because of its small genome, Arabidopsis thaliana serves as a powerful system for understanding the role of various histone modifications in a complex organism, notably in association with DNA methylation and in relation to the epigenetic inheritance of silent chromatin(4). Here we describe a chromatin immunoprecipitation (ChIP) protocol developed for A. thaliana that permits, in combination with hybridization to genomic tiling microarrays, the mapping of histone modifications with high resolution along large genomic regions(5). After cross-linking, chromatin is immunoprecipitated using antibodies directed against specific histone modifications. DNA recovered from the precipitate is amplified, Labeled, hybridized to microarrays and compared to total DNA. This protocol has been used successfully to map histone H3 methylated at Lys4 or Lys9 across a 1.5-Mb region(5) and should have broad applications in plants and other organisms. A protocol that outlines the profiling of DNA methylation patterns at similar high resolution has also been developed(6).

Published
2005
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26. Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics

Author

Gisèle Butterlin, D. Claux, Anne-Françoise Adam-Blondon, C. Roux, Patrice This, Didier Merdinoglu, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), and Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I

Subjects
Electrophoresis, 0106 biological sciences, Population, Minisatellite Repeats, Breeding, Quantitative trait locus, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Species Specificity, Gene mapping, Genotype, Genetics, Vitis, education, Crosses, Genetic, DNA Primers, 030304 developmental biology, Linkage (software), [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, education.field_of_study, Chromosome Mapping, food and beverages, Selfing, Agriculture, General Medicine, Microsatellite, France, Nucleic Acid Amplification Techniques, Agronomy and Crop Science, Genome, Plant, 010606 plant biology & botany, Biotechnology
Abstract

International audience; The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome (n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals (S x G population), successfully amplifying 310 markers. Of these, 88.4% markers were heterozygous for at least one of the two parents. A total of 292 primer pairs were then tested on Riesling, the parent of the RS1 population derived from selfing (96 individuals), successfully amplifying 299 markers among which 207 (62.9%) were heterozygous. Only 6.7% of the markers were homozygous in all three genotypes, stressing the interest of such markers in grape genetics. Four maps were constructed based on the segregation of 245 SSR markers in the two populations. The Syrah map was constructed from the segregations of 177 markers that could be ordered into 19 linkage groups (total length 1,172.2 cM). The Grenache map was constructed with the segregations of 178 markers that could be ordered into 18 linkage groups (total length 1,360.6 cM). The consensus S x G map was constructed with the segregations of 220 markers that were ordered into 19 linkage groups (total length 1,406.1 cM). One hundred and eleven markers were scored on the RS1 population, among them 27 that were not mapped using the S x G map. Out of these 111 markers, 110 allowed to us to construct a map of a total length of 1,191.7 cM. Using these four maps, the genome length of V. vinifera was estimated to be around 2,200 cM. The present work allowed us to map 123 new SSR markers on the V. vinifera genome that had not been ordered in a previous SSR-based map (Riaz et al. 2004), representing an average of 6.5 new markers per linkage group. Any new SSR marker mapped is of great potential usefulness for many applications such as the transfer of well-scattered markers to other maps for QTL detection, the use of markers in specific regions for the fine mapping of genes/QTL, or for the choice of markers for MAS

Published
2004
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27. Droplet suction on porous media

Author

F. Brochard-Wyart, Laurent Bacri, Analyse et environnement (LAE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), inconnu, and Inconnu

Subjects
Materials science, Biophysics, Spherical cap, 02 engineering and technology, 01 natural sciences, Physics::Geophysics, Physics::Fluid Dynamics, Contact angle, Optics, 0103 physical sciences, General Materials Science, Soft matter, 010304 chemical physics, business.industry, Drop (liquid), Surfaces and Interfaces, General Chemistry, Mechanics, 021001 nanoscience & nanotechnology, Membrane, Constant current, 0210 nano-technology, business, Porous medium, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], Quasistatic process, Biotechnology
Abstract

We study the forced aspiration of small ( mm) and large ( cm) liquid drops, deposited on prewetted porous membranes, and pumped mechanically with a constant current J. Two kinds of membranes are used where the pores are i) disconnected, cylindrical and calibrated or ii) interconnected “sponge-like”. Whatever the size of the drops and the intensity J of the current, two suction regimes are observed versus time: 1) a “locked” regime, when the drop is pinned, with a dynamic contact angle decreasing from advancing ( ) to finite receding ( ) contact angle; 2) an “unlocked” regime, where the contour line recedes with a constant contact angle closed to . In both regimes, the shape of the drop remains quasistatic, during the suction process, i.e. a spherical cap for small drops and a flat “gravity pancake” for large ones.

Published
2000
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28. MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates

Author

Marie-Laure Martin-Magniette, Michael Seifert, Caroline Bérard, Tristan Mary-Huard, Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Ctr Informat Serv & High Performance Comp, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Ctr Biotechnol, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), MIA department of INRA, BAP department of INRA, MICA department of INRA, TAG ANR/Genoplante project, DAAD PROCOPE [50748812], AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU), Technische Universität Dresden (TUD), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Chromatin Immunoprecipitation, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, 01 natural sciences, Biochemistry, Data modeling, Histones, 03 medical and health sciences, ARABIDOPSIS, STATES, Structural Biology, Molecular Biology, Oligonucleotide Array Sequence Analysis, Plant Proteins, 030304 developmental biology, Genetics, 0303 health sciences, Tiling array, Models, Genetic, Applied Mathematics, Linear model, Nucleic Acid Hybridization, Mixture model, Chip, Computer Science Applications, ChIP-sequencing, Linear Models, DNA microarray, Biological system, Chromatin immunoprecipitation, Software, 010606 plant biology & botany
Abstract

Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. The robust identification of ChIP-enriched regions is frequently complicated by noisy measurements. This identification can be improved by accounting for dependencies between adjacent probes on chromosomes and by modeling of biological replicates. MultiChIPmixHMM is a user-friendly R package to analyse ChIP-chip data modeling spatial dependencies between directly adjacent probes on a chromosome and enabling a simultaneous analysis of replicates. It is based on a linear regression mixture model, designed to perform a joint modeling of immunoprecipitated and input measurements. We show the utility of MultiChIPmixHMM by analyzing histone modifications of Arabidopsis thaliana. MultiChIPmixHMM is implemented in R and including functions in C, freely available from the CRAN web site: http://cran.r-project.org .

Published
2013
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29. A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome

Author

Marc Bartoli, Jean-Baptiste Boucheteil, Sylvie Marchand, Azeddine Bentaïb, Nathalie Daniele, Karine Charton, Gaëlle Blandin, Evelyne Gicquel, Laetitia Barrault, Daniel Stockholm, Isabelle Richard, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the Association Française contre les Myopathies and the Jain Foundation., BMC, Ed., and Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
musculoskeletal diseases, Candidate gene, Interactome, Muscular dystrophies, Two-hybrid screening, Systems biology, Computational biology, Telethonin, Bioinformatics, Dysferlin, 03 medical and health sciences, 0302 clinical medicine, Interaction network, Orthopedics and Sports Medicine, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Molecular Biology, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, biology, Research, Cell Biology, Yeast-two hybrid, biology.protein, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], 030217 neurology & neurosurgery
Abstract

Background The complexity of the skeletal muscle and the identification of numerous human disease-causing mutations in its constitutive proteins make it an interesting tissue for proteomic studies aimed at understanding functional relationships of interacting proteins in both health and diseases. Method We undertook a large-scale study using two-hybrid screens and a human skeletal-muscle cDNA library to establish a proteome-scale map of protein-protein interactions centered on proteins involved in limb-girdle muscular dystrophies (LGMD). LGMD is a group of more than 20 different neuromuscular disorders that principally affect the proximal pelvic and shoulder girdle muscles. Results and conclusion The interaction network we unraveled incorporates 1018 proteins connected by 1492 direct binary interactions and includes 1420 novel protein-protein interactions. Computational, experimental and literature-based analyses were performed to assess the overall quality of this network. Interestingly, LGMD proteins were shown to be highly interconnected, in particular indirectly through sarcomeric proteins. In-depth mining of the LGMD-centered interactome identified new candidate genes for orphan LGMDs and other neuromuscular disorders. The data also suggest the existence of functional links between LGMD2B/dysferlin and gene regulation, between LGMD2C/γ-sarcoglycan and energy control and between LGMD2G/telethonin and maintenance of genome integrity. This dataset represents a valuable resource for future functional investigations.

Published
2013
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30. Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

Author

Antoine Kremer, Clément Boussardon, Patricia Faivre Rampant, Catherine Bodénès, Isabelle Lesur, Grégoire Le Provost, Christophe Plomion, Marie-Laure Martin-Magniette, Sylvia Fluch, Hélène Bergès, Frédérique Bitton, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Austrian Institute of Technology (AIT), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
0106 biological sciences, Chromosomes, Artificial, Bacterial, Cytoplasm, lcsh:QH426-470, DNA, Plant, lcsh:Biotechnology, Forest management, Genomics, Minisatellite Repeats, 01 natural sciences, Genome, DNA sequencing, Quercus robur, Quercus, 03 medical and health sciences, lcsh:TP248.13-248.65, Genetic variation, Genetics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genomic Library, 0303 health sciences, biology, Chromosome Mapping, Molecular Sequence Annotation, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, lcsh:Genetics, Genetic marker, Evolutionary biology, DNA microarray, Genome, Plant, Research Article, 010606 plant biology & botany, Biotechnology
Abstract

Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The Eco RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.

Published
2011
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31. Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes

Author

Nathalie Ningre, Sandrine Balzergue, David Cohen, Jean-Pierre Renou, Marie-Laure Martin-Magniette, Emilie Tisserant, Didier Le Thiec, Irène Hummel, Marie-Béatrice Bogeat-Triboulot, Jean-Philippe Tamby, Gaëlle Lelandais, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Interactions Arbres-Microorganismes (IAM), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), This work was funded and DC was supported by the project ANR GENOPLANTE 'POPSEC' (GPLA06028G). Part of this work was also funded by a Region Lorraine grant (# 12000160)., ANR-06-GPLA-0007,POPSEC,POPSEC : Molecular bases of acclimation and adaptation to water deficit in poplar(2006), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, BMC, Ed., Réseau de Génomique végétale - GENOPLANTE 2010 - POPSEC : Molecular bases of acclimation and adaptation to water deficit in poplar - - POPSEC2006 - ANR-06-GPLA-0007 - GPLA - VALID, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA), ANR-06-GPLA-0007,GPLA06028G,POPSEC : Molecular bases of acclimation and adaptation to water deficit in poplar(2006), and Bogeat-Triboulot, Marie-Béatrice

Subjects
MESH: Genome, Plant, 0106 biological sciences, Transcription, Genetic, genotype, Plant genetics, MESH: Genetic Markers, 01 natural sciences, Genome, genomic, MESH: Genotype, Transcriptome, Gene Expression Regulation, Plant, MESH: Genes, Plant, Cluster Analysis, Gene Regulatory Networks, MESH: Ecosystem, MESH: Organ Specificity, MESH: Meristem, MESH: Gene Regulatory Networks, 2. Zero hunger, Genetics, 0303 health sciences, food and beverages, Droughts, MESH: Plant Leaves, Populus, Organ Specificity, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genome, Plant, Research Article, Biotechnology, Genetic Markers, lcsh:QH426-470, lcsh:Biotechnology, Meristem, MESH: Droughts, Drought tolerance, Genomics, MESH: Molecular Sequence Annotation, Biology, Genes, Plant, MESH: Gene Expression Profiling, 03 medical and health sciences, Meta-Analysis as Topic, comparative transcriptomics, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, MESH: Meta-Analysis as Topic, MESH: Gene Expression Regulation, Plant, Ecosystem, 030304 developmental biology, Comparative genomics, Gene Expression Profiling, MESH: Transcription, Genetic, fungi, Molecular Sequence Annotation, MESH: Cluster Analysis, Plant Leaves, meta-analysis, Gene expression profiling, lcsh:Genetics, MESH: Populus, 010606 plant biology & botany
Abstract

BackgroundComparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from otherPopulusspecies.ResultsUsing a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought.ConclusionsIn poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.

Published
2010
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32. Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance

Author

Fanny Ramel, Jean-Pierre Renou, Francisco Cabello-Hurtado, Cécile Sulmon, Ivan Couée, Marie-Laure Martin-Magniette, Abdelhak El Amrani, Ludivine Taconnat, Gwenola Gouesbet, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Martin-Magniette, Marie-Laure, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Transcription, Genetic, Arabidopsis, 01 natural sciences, chemistry.chemical_compound, herbicide, Gene Expression Regulation, Plant, Gene expression, oxidative stress, Atrazine, 2. Zero hunger, Genetics, adaptation physiological, 0303 health sciences, Gene Expression Regulation, Developmental, sucrose, Adaptation, Physiological, Cell biology, sucre, Signal transduction, Genome, Plant, signal transduction, Research Article, Biotechnology, lcsh:QH426-470, arabidopsis proteins, lcsh:Biotechnology, [SDE.MCG]Environmental Sciences/Global Changes, gene expression, Biology, 03 medical and health sciences, lcsh:TP248.13-248.65, Gene family, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Gene, 030304 developmental biology, Herbicides, Gene Expression Profiling, arabidopsis thaliana, biology.organism_classification, Gene expression profiling, lcsh:Genetics, chemistry, Seedlings, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Xenobiotic, 010606 plant biology & botany
Abstract

Background Soluble sugars, which play a central role in plant structure and metabolism, are also involved in the responses to a number of stresses, and act as metabolite signalling molecules that activate specific or hormone-crosstalk transduction pathways. The different roles of exogenous sucrose in the tolerance of Arabidopsis thaliana plantlets to the herbicide atrazine and oxidative stress were studied by a transcriptomic approach using CATMA arrays. Results Parallel situations of xenobiotic stress and sucrose-induced tolerance in the presence of atrazine, of sucrose, and of sucrose plus atrazine were compared. These approaches revealed that atrazine affected gene expression and therefore seedling physiology at a much larger scale than previously described, with potential impairment of protein translation and of reactive-oxygen-species (ROS) defence mechanisms. Correlatively, sucrose-induced protection against atrazine injury was associated with important modifications of gene expression related to ROS defence mechanisms and repair mechanisms. These protection-related changes of gene expression did not result only from the effects of sucrose itself, but from combined effects of sucrose and atrazine, thus strongly suggesting important interactions of sucrose and xenobiotic signalling or of sucrose and ROS signalling. Conclusion These interactions resulted in characteristic differential expression of gene families such as ascorbate peroxidases, glutathione-S-transferases and cytochrome P450s, and in the early induction of an original set of transcription factors. These genes used as molecular markers will eventually be of great importance in the context of xenobiotic tolerance and phytoremediation.

Published
2007
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33. Inferring biological networks with output kernel trees

Author

Pierre Geurts, Florence d'Alché-Buc, Nizar Touleimat, Marie Dutreix, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Conception synthèse et étude d'antitumoraux, Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Applied Mathematics and Computer Science [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Université d'Évry-Val-d'Essonne (UEVE), and Universiteit Gent = Ghent University (UGENT)

Subjects
Time Factors, Proteome, [SDV]Life Sciences [q-bio], Metabolic network, 02 engineering and technology, computer.software_genre, Biochemistry, Pattern Recognition, Automated, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Structural Biology, 0202 electrical engineering, electronic engineering, information engineering, Diffusion kernel, ComputingMilieux_MISCELLANEOUS, [STAT.AP]Statistics [stat]/Applications [stat.AP], 0303 health sciences, Systems Biology, Applied Mathematics, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Complement (complexity), [STAT]Statistics [stat], Kernel (statistics), Regression Analysis, 020201 artificial intelligence & image processing, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Algorithms, Signal Transduction, Systems biology, [SCCO.COMP]Cognitive science/Computer science, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Machine learning, Models, Biological, 03 medical and health sciences, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Artificial Intelligence, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Computer Simulation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Focus (computing), [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], business.industry, Research, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Gene Expression Regulation, ComputingMethodologies_GENERAL, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Biological network
Abstract

International audience; Background Elucidating biological networks between proteins appears nowadays as one of the most important challenges in systems biology. Computational approaches to this problem are important to complement high-throughput technologies and to help biologists in designing new experiments. In this work, we focus on the completion of a biological network from various sources of experimental data. Results We propose a new machine learning approach for the supervised inference of biological networks, which is based on a kernelization of the output space of regression trees. It inherits several features of tree-based algorithms such as interpretability, robustness to irrelevant variables, and input scalability. We applied this method to the inference of two kinds of networks in the yeast S. cerevisiae: a protein-protein interaction network and an enzyme network. In both cases, we obtained results competitive with existing approaches. We also show that our method provides relevant insights on input data regarding their potential relationship with the existence of interactions. Furthermore, we confirm the biological validity of our predictions in the context of an analysis of gene expression data. Conclusion Output kernel tree based methods provide an efficient tool for the inference of biological networks from experimental data. Their simplicity and interpretability should make them of great value for biologists.

Published
2007
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34. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)

Author

Sandrine Balzergue, Jérôme Salse, Carole Confolent, Florent Murat, Caroline Pont, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), INRA ('Genetique et Amelioration des Plantes', reference 'Appel d'Offre Transcriptome'), Agence Nationale de la Recherche [ANR-09-JCJC 0058 01], ANR Blanc-PAGE [ANR 2011 BSV6 00801], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
COMPARATIVE GENOMICS, EXPRESSION, 0106 biological sciences, [SDV]Life Sciences [q-bio], UniGene, RNA-Seq, Biology, Genes, Plant, Synteny, SEQUENCE, 01 natural sciences, Genome, Chromosomes, Plant, 03 medical and health sciences, Genes, Duplicate, RICE, TRANSCRIPTOME, DUPLICATED GENES, HEXAPLOWHEAT, VERTEBRATE EVOLUTION, MAIZE GENOME, ARABIDOPSIS, Triticeae, Gene, Phylogeny, Triticum, 030304 developmental biology, 2. Zero hunger, Genetics, Comparative genomics, 0303 health sciences, Ploidies, Sequence Analysis, RNA, Research, Genetic Variation, food and beverages, Bread, biology.organism_classification, Biological Evolution, Multigene Family, Subfunctionalization, Brachypodium distachyon, Brachypodium, 010606 plant biology & botany
Abstract

Background: Whole genome duplication is a common evolutionary event in plants. Bread wheat (Triticum aestivum L.) is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes. Results: We performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a set of 37,695 non-redundant sequence clusters, which is an unprecedented resolution corresponding to an estimated half of the wheat genome unigene repertoire. Using the Brachypodium distachyon genome as a reference for the Triticeae, we classified gene clusters into orthologous, paralogous, and homoeologous relationships. Based on this wheat gene evolutionary classification, older duplicated copies (dating back 50 to 70 million years) exhibit more than 80% gene loss and expression divergence while recent duplicates (dating back 1.5 to 3 million years) show only 54% gene loss and 36 to 49% expression divergence. Conclusions: We suggest that structural shuffling due to duplicated gene loss is a rapid process, whereas functional shuffling due to neo- and/or subfunctionalization of duplicates is a longer process, and that both shuffling mechanisms drive functional redundancy erosion. We conclude that, as a result of these mechanisms, half the gene duplicates in plants are structurally and functionally altered within 10 million years of evolution, and the diploidization process is completed after 45 to 50 million years following polyploidization.

Published
2011
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35. Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny

Author

Olivier Panaud, Pierre Capy, Alan H. Schulman, Aurélie Hua-Van, Michele Morgante, Andrew Flavell, Boulos Chalhoub, Etienne Paux, Jeffrey L. Bennetzen, François Sabot, Phillip SanMiguel, Philippe Leroy, Thomas Wicker, Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Viikki Biocenter, Institute of Biotechnology, MTT/BI Plant Genomics Laboratory, Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), Department of Genetics, University of Georgia [USA], Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), SCRI, Plant Research Unit, University of Dundee, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine - University of Udine [Italie], Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Genomics Core Facility, Purdue University [West Lafayette], Agrifood Research Finland, Universität Zürich [Zürich] (UZH), UPR 9034, Laboratoire Evolution, Génomes et Spéciation, and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Transposable element, Genetics, 0303 health sciences, STRUCTURE DU GENOME, [SDV]Life Sciences [q-bio], ELEMENT TRANSPOSABLE ADN, food and beverages, Computational biology, GENETIQUE, Gene mutation, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Transposition (music), 03 medical and health sciences, Annotation, Phylogenetics, Identification (biology), Molecular Biology, Genetics (clinical), 030304 developmental biology, Sequence (medicine)
Abstract

Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.

Published
2009
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