Author: "François Artiguenave" / Topic: gene - Searchworks@Jio Institute Digital Library Search Results

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27 results on '"François Artiguenave"'

1. Genomic Investigation of Balanced Chromosomal Rearrangements in Patients with Abnormal Phenotypes

Author: François Artiguenave, Vera Lúcia Gil-da-Silva-Lopes, Andréa Trevas Maciel-Guerra, Isabella Lopes Monlleó, Ilária Cristina Sgardioli, Carlos Eduardo Steiner, Vincent Meyer, Milena Simioni, and Nilma Lúcia Viguetti-Campos
Subjects: 0301 basic medicine, Genetics, Breakpoint, breakpoint cluster region, Chromosomal translocation, Karyotype, Chromosomal rearrangement, Biology, Genome, DNA sequencing, 03 medical and health sciences, 030104 developmental biology, Original Article, Gene, Genetics (clinical)
Abstract: Balanced chromosomal rearrangements (BCR) are associated with abnormal phenotypes in approximately 6% of balanced translocations and 9.4% of balanced inversions. Abnormal phenotypes can be caused by disruption of genes at the breakpoints, deletions, or positional effects. Conventional cytogenetic techniques have a limited resolution and do not enable a thorough genetic investigation. Molecular techniques applied to BCR carriers can contribute to the characterization of this type of chromosomal rearrangement and to the phenotype-genotype correlation. Fifteen individuals among 35 with abnormal phenotypes and BCR were selected for further investigation by molecular techniques. Chromosomal rearrangements involved 11 reciprocal translocations, 3 inversions, and 1 balanced insertion. Array genomic hybridization (AGH) was performed and genomic imbalances were detected in 20% of the cases, 1 at a rearrangement breakpoint and 2 further breakpoints in other chromosomes. Alterations were further confirmed by FISH and associated with the phenotype of the carriers. In the analyzed cases not showing genomic imbalances by AGH, next-generation sequencing (NGS), using whole genome libraries, prepared following the Illumina TruSeq DNA PCR-Free protocol (Illumina®) and then sequenced on an Illumina HiSEQ 2000 as 150-bp paired-end reads, was done. The NGS results suggested breakpoints in 7 cases that were similar or near those estimated by karyotyping. The genes overlapping 6 breakpoint regions were analyzed. Follow-up of BCR carriers would improve the knowledge about these chromosomal rearrangements and their consequences.
Published: 2017

2. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Author: Pasqua Veronico, Emeline Deleury, Francesca De Luca, Magali Esquibet, Patrick Wincker, Thomas J. Baum, Tom R. Maier, Erika Sallet, Jonathan J. Ewbank, Edgardo Ugarte, Cyril Van Ghelder, Marie-Noëlle Rosso, Delphine Steinbach, Marie-Cécile Caillaud, Jean Weissenbach, Véronique Anthouard, Pedro M. Coutinho, Mark Blaxter, Jean-Marc Aury, Marc Robinson-Rechavi, Pierre Abad, Geert Smant, Timothé Flutre, Hadi Quesneville, Gabriel V. Markov, Paul McVeigh, Jérôme Gouzy, Philippe Castagnone-Sereno, Corinne Dasilva, Etienne Danchin, Paola Leonetti, Aaron G. Maule, Marc Magliano, Béatrice Ségurens, John T. Jones, Eric L. Davis, Laetitia Perfus-Barbeoch, Claire Jubin, Thomas Schiex, Vincent Laudet, Florence Deau, Olivier Jaillon, François Artiguenave, Eric Grenier, Tarek Hewezi, Bruno Favery, Teresa Bleve-Zacheo, T.O.G. Tytgat, Bernard Henrissat, Noureddine Hamamouch, Graziano Pesole, Jared V. Goldstone, Julie Poulain, Vivian C. Blok, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-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), Interactions plantes-microorganismes et santé végétale (IPMSV), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-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), Scottish Crop Research Institute, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Istituto per la Protezione delle Piante, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Unité de Recherche Génomique Info (URGI), Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), Department of Plant Pathology, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Iowa State University (ISU), School of Biological Sciences, Dipartimento di Biochimica e Biologia moleculare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Department of Ecology and Evolution, Université de Lausanne = University of Lausanne (UNIL), Laboratory of Nematology, Wageningen University and Research [Wageningen] (WUR), Institute of Evolutionary Biology, University of Edinburgh, University of North Carolina System (UNC), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, School of Biolgical Sciences, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 1064 UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Institut National de la Recherche Agronomique (INRA)-Santé des plantes et environnement (S.P.E.)-UMR INRA / CNRS / Univ. Nice (Univ.SA) : Interactions Plantes Microorganismes et Santé Végétale, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Consiglio Nazionale delle Ricerche [Roma] (CNR), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Università degli studi di Bari, Université de Lausanne (UNIL), Wageningen University and Research Centre [Wageningen] (WUR), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Unité de Biométrie et Intelligence Artificielle (UBIA), 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), 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), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), 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), and Università degli studi di Bari Aldo Moro (UNIBA)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Helminth genetics, 01 natural sciences, Applied Microbiology and Biotechnology, Genome, Plant Roots, Meloidogyne incognita, ADAPTATION, genes, root-knot nematodes, Genes, Helminth, 2. Zero hunger, Expressed Sequence Tags, 0303 health sciences, biology, plant-parasitic nematode, EPS-2, Chromosome Mapping, GENOME SEQUENCE, food and beverages, DNA, Helminth, Plants, bdelloid rotifers, MELOIDOGYNE INCOGNITA, PARTHENOGENETIC NEMATODE, Molecular Medicine, RNA Interference, Terra incognita, Biotechnology, DNA, Complementary, Sequence analysis, Molecular Sequence Data, Biomedical Engineering, cloning, Bioengineering, phytopathogenic bacteria, 03 medical and health sciences, Botany, expression, Animals, Tylenchoidea, Gene, Laboratorium voor Nematologie, 030304 developmental biology, Plant Diseases, Whole genome sequencing, PLANT PARASITISM, Genome, Helminth, Base Sequence, Sequence Analysis, DNA, prediction, biology.organism_classification, caenorhabditis-elegans, Nematode, Evolutionary biology, identification, Laboratory of Nematology, protein, Sequence Alignment, 010606 plant biology & botany
Abstract: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies
Published: 2008
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3. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

Author: Frédéric Partensky, Patrick Wincker, Kira S. Makarova, Alexis Dufresne, Catherine Robert, Igor B. Rogozin, Jean Weissenbach, Marcel Salanoubat, Nicole Tandeau de Marsac, Martin Ostrowski, Ilka M. Axmann, David J. Scanlan, Florence Le Gall, Eugene V. Koonin, Yuri I. Wolf, Michael Y. Galperin, Valérie Barbe, François Artiguenave, Sophie Oztas, Simone Duprat, and Wolfgang R. Hess
Subjects: Chlorophyll, DNA, Bacterial, Genome evolution, DNA Repair, Oceans and Seas, Citric Acid Cycle, Molecular Sequence Data, Marine Biology, Biology, Cyanobacteria, Genome, Open Reading Frames, Cell Wall, Gene density, Photosynthesis, Gene, Genome size, Gene Rearrangement, Whole genome sequencing, Genetics, Base Composition, Multidisciplinary, Nucleotides, Adaptation, Physiological, Housekeeping gene, Phytoplankton, Commentary, RRNA Operon, Genome, Bacterial, Signal Transduction
Abstract: Prochlorococcus marinus , the dominant photosynthetic organism in the ocean, is found in two main ecological forms: high-light-adapted genotypes in the upper part of the water column and low-light-adapted genotypes at the bottom of the illuminated layer. P. marinus SS120, the complete genome sequence reported here, is an extremely low-light-adapted form. The genome of P. marinus SS120 is composed of a single circular chromosome of 1,751,080 bp with an average G+C content of 36.4%. It contains 1,884 predicted protein-coding genes with an average size of 825 bp, a single rRNA operon, and 40 tRNA genes. Together with the 1.66-Mbp genome of P. marinus MED4, the genome of P. marinus SS120 is one of the two smallest genomes of a photosynthetic organism known to date. It lacks many genes that are involved in photosynthesis, DNA repair, solute uptake, intermediary metabolism, motility, phototaxis, and other functions that are conserved among other cyanobacteria. Systems of signal transduction and environmental stress response show a particularly drastic reduction in the number of components, even taking into account the small size of the SS120 genome. In contrast, housekeeping genes, which encode enzymes of amino acid, nucleotide, cofactor, and cell wall biosynthesis, are all present. Because of its remarkable compactness, the genome of P. marinus SS120 might approximate the minimal gene complement of a photosynthetic organism.
Published: 2003
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4. Genomic Exploration of the Hemiascomycetous Yeasts: 12. Kluyveromyces marxianus var. marxianus

Author: Patrick Wincker, François Artiguenave, Bernard Dujon, Bertrand Llorente, Gaëlle Blandin, and Alain Malpertuy
Subjects: Retroelements, Intron, Saccharomyces cerevisiae, Biophysics, Retrotransposon, Paralogous Gene, Biology, DNA, Mitochondrial, DNA, Ribosomal, Synteny, Biochemistry, Genome, Fungal Proteins, Contig Mapping, Kluyveromyces, Open Reading Frames, Ascomycota, RNA, Transfer, Kluyveromyces marxianus, Structural Biology, Genetics, Genomic library, Codon, tRNA, Molecular Biology, Gene, Conserved Sequence, Comparative genomics, Base Sequence, Chromosome Mapping, Nuclear Proteins, Cell Biology, biology.organism_classification, Introns, Genetic Code, Multigene Family, Spliceosomes, Chromosomes, Fungal, Genome, Fungal
Abstract: As part of the comparative genomics project ‘GENOLEVURES’, we studied the Kluyveromyces marxianus var. marxianus strain CBS712 using a partial random sequencing strategy. With a 0.2×genome equivalent coverage, we identified ca. 1300 novel genes encoding proteins, some containing spliceosomal introns with consensus splice sites identical to those of Saccharomyces cerevisiae, 28 tRNA genes, the whole rDNA repeat, and retrotransposons of the Ty1/2 family of S. cerevisiae with diverged Long Terminal Repeats. Functional classification of the K. marxianus genes, as well as the analysis of the paralogous gene families revealed few differences with respect to S. cerevisiae. Only 42 K. marxianus identified genes are without detectable homolog in the baker’s yeast. However, we identified several genetic rearrangements between these two yeast species.
Published: 2000
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5. Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae

Author: Michel Aigle, Gaëlle Blandin, Patrick Wincker, Micheline Wésolowski-Louvel, Elisabeth Bon, Monique Bolotin-Fukuhara, Fredj Tekaia, Jean-Luc Souciet, Odile Ozier-Kalogeropoulos, Cécile Neuvéglise, Claude Gaillardin, Serge Potier, Philippe Brottier, Jean Weissenbach, William Saurin, François Artiguenave, Bernard Dujon, Claire Toffano-Nioche, Jacky de Montigny, Serge Casaregola, Alain Malpertuy, Pascal Durrens, Bertrand Llorente, and Andrée Lépingle
Subjects: Duplication, Saccharomyces cerevisiae, Biophysics, Translocation, Biology, Biochemistry, Genome, Deletion, Redundancy, Ascomycota, Structural Biology, Molecular evolution, Gene Duplication, Gene Order, Gene duplication, Genetics, Molecular Biology, Gene, Synteny, Chromosomal inversion, Inversion, Chromosome Mapping, Computational Biology, Chromosome, Genomics, Cell Biology, biology.organism_classification, Loss, Chromosomes, Fungal, Gene Deletion
Abstract: We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events.
Published: 2000
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6. Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies1

Author: Jean Weissenbach, Patrick Wincker, Philippe Brottier, Monique Bolotin-Fukuhara, Micheline Wésolowski-Louvel, Michel Aigle, Cécile Neuvéglise, Fredj Tekaia, Claire Toffano-Nioche, Claude Gaillardin, Jacky de Montigny, Bernard Dujon, Odile Ozier-Kalogeropoulos, Gaëlle Blandin, Serge Casaregola, Serge Potier, Alain Malpertuy, Elisabeth Bon, Pascal Durrens, Bertrand Llorente, Andrée Lépingle, William Saurin, Jean-Luc Souciet, and François Artiguenave
Subjects: Genetics, Comparative genomics, Genome evolution, Sequence analysis, Biophysics, Cell Biology, Computational biology, Biology, Biochemistry, Genome, Structural Biology, Phylogenetics, Molecular evolution, Molecular Biology, Gene, Genome size
Abstract: The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast-specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Genolevures’.
Published: 2000
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7. Genomic Exploration of the Hemiascomycetous Yeasts: 11.Kluyveromyces lactis

Author: Michel Termier, Robert Montrocher, Roland Marmeisse, Patrick Wincker, Marc Lemaire, Monique Bolotin-Fukuhara, Claire Toffano-Nioche, Catherine Robert, François Artiguenave, Guillemette Duchateau-Nguyen, and Micheline Wésolowski-Louvel
Subjects: Centromere, Molecular Sequence Data, Saccharomyces cerevisiae, Gene Dosage, Biophysics, Synteny, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Genome, Fungal Proteins, Kluyveromyces, Open Reading Frames, Complete sequence, Plasmid, Ascomycota, RNA, Transfer, Structural Biology, Gene Order, Genetics, ORFS, Molecular Biology, Gene, Kluyveromyces lactis, Sequence Homology, Amino Acid, biology, Cell Biology, biology.organism_classification, Mitochondrial DNA, Random sequencing, Open reading frame, DNA Transposable Elements, Chromosomes, Fungal, Genome, Fungal, Gene function, Plasmids
Abstract: Random sequencing of the Kluyveromyces lactis genome allowed the identification of 2235–2601 open reading frames (ORFs) homologous to S. cerevisiae ORFs, 51 ORFs which were homologous to genes from other species, 64 tRNAs, the complete rDNA repeat, and a few Ty1- and Ty2-like sequences. In addition, the complete sequence of plasmid pKD1 and a large coverage of the mitochondrial genome were obtained. The global distribution into general functional categories found in Saccharomyces cerevisiae and as defined by MIPS is well conserved in K. lactis. However, detailed examination of certain subcategories revealed a small excess of genes involved in amino acid metabolism in K. lactis. The sequences are deposited at EMBL under the accession numbers AL424881–AL430960.
Published: 2000
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8. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

Author: Tristan Barbeyron, Wilfrid Carré, Michael Katinka, Loraine Brillet, Klaus Valentin, Karine Labadie, Betina M. Porcel, Zofia Nehr, Francisco Cabello-Hurtado, Mirjam Czjzek, Benjamin Noel, Philippe Deschamps, Susana M. Coelho, John H. F. Bothwell, Pascal J. Lopez, Marek Eliáš, François Artiguenave, François-Yves Bouget, Thierry Tonon, Jean Weissenbach, Christophe Colleoni, Deirdre H. McLachlan, Ahmed A. Moustafa, Cécile Hervé, Olivier Panaud, Catherine Boyen, Jonas Collén, Antonios Zambounis, Frédéric Partensky, Cristian Chaparro, Ludovic Delage, Jose Fernandes Barbosa-Neto, Salvador Capella-Gutierrez, Bernard Kloareg, Nathalie Kowalczyk, Gaelle Samson, Gurvan Michel, Simon M. Dittami, Jean-Marc Aury, J. Mark Cock, Patrick Wincker, Agnès Groisillier, Pi Nyvall Collén, Bénédicte Charrier, Corinne Da Silva, Catherine Leblanc, Lionel Cladière, Alok Arun, Laurence Meslet-Cladiere, Claire M. M. Gachon, Sylvie Rousvoal, Kamel Jabbari, Stefan A. Rensing, Toni Gabaldón, Steven G. Ball, Aikaterini Symeonidi, Julie Poulain, Végétaux marins et biomolécules, 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)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), 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), Commissariat à l'Energie Atomique, 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), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Department of Plant Physiology, Faculty of Sciences, Charles University [Prague] (CU), Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), 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), 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), Universitat Pompeu Fabra [Barcelona] (UPF), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Scottish Association for Marine Science (SAMS), 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), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, University of Freiburg [Freiburg], Freiburg Initiative in Systems Biology, Centre for Research and Technology Hellas (CERTH), 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)), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Charles University [Prague], 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), Universitat Pompeu Fabra [Barcelona], Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Center for Research and Technology Hellas, 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, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), 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), 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), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-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)-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 Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB), 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 Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), and Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Transposable element, Genome evolution, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Bacterial genome size, Biology, Chondrus, MESH: Base Sequence, MESH: RNA, Plant, Genes, Plant, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Genes, Plant, 14. Life underwater, Gene, Genome size, MESH: Evolution, Molecular, 030304 developmental biology, Plant Proteins, Genetics, 0303 health sciences, Multidisciplinary, MESH: Molecular Sequence Data, Base Sequence, MESH: Plant Proteins, Archaeplastida, Biological Sciences, biology.organism_classification, MicroRNAs, RNA, Plant, MESH: MicroRNAs, MESH: Chondrus, 010606 plant biology & botany
Abstract: Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
Published: 2013
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9. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining

Author: Pierre Abad, Etienne Danchin, Amandine Campan-Fournier, Nicolas Nottet, Marc Magliano, François Artiguenave, Martine Da Rocha, Marie-Jeanne Arguel, Karine Labadie, Laetitia Perfus-Barbeoch, Julie Guy, Corinne Da Silva, Marie-Noëlle Rosso, Danchin, Etienne, Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), 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), ANR NEMATARGETS, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, interférence à arn, parasitisme, 01 natural sciences, Genome, RNA interference, gène cible, Meloidogyne incognita, nématode à galles, lcsh:QH301-705.5, protéome, pathologie végétale, Genes, Helminth, gène régulateur, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, Effector, Pan-genome, food and beverages, santé humaine, nématicide, Agricultural sciences, lutte contre les ravageurs, ravageur de culture, pollution environnementale, RNA Interference, Research Article, lcsh:Immunologic diseases. Allergy, nématode des plantes, Immunology, phytopathologie, Biology, approche génomique, Microbiology, identification de gènes, nématode parasite, 03 medical and health sciences, interaction plante parasite, Virology, Botany, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, séquence silencer, Tylenchoidea, Molecular Biology, Gene, Plant Diseases, 030304 developmental biology, Comparative genomics, biology.organism_classification, meloidogyne incognita, Nematode, lcsh:Biology (General), génie génétique, Parasitology, lcsh:RC581-607, Sciences agricoles, Biologie végétale, Genome-Wide Association Study, 010606 plant biology & botany
Abstract: Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when silenced, constitute promising targets for the development of more specific and safer control means., Author Summary Plant-parasitic nematodes are annually responsible for more than $100 billion crop yield loss worldwide and those considered as causing most of the damages are root-knot nematodes. These nematodes used to be controlled by chemicals that are now banned from use because of their poor specificity and high toxicity for the environment and human health. In the absence of sustainable alternative solutions, new control means, more specifically targeted against these nematodes and safe for the environment are needed. We searched in root-knot nematode genomes, genes conserved in various plant-damaging species while otherwise absent from the genomes of non target species such as those of chordates, plants, annelids, insect pollinators and mollusks. These genes are probably important for plant parasitism and their absence from non-target species make them interesting candidates for the development of more specific and safer control means. Further bioinformatics pruning of this set of genes yielded 16 novel candidates that could be biologically tested. Using RNA interference, we knocked down each of these 16 genes in a root-knot nematode and tested the effect on plant parasitism efficiency. Out of the 16 tested genes, 12 showed a significant and reproducible diminution of infestation when silenced and are thus particularly promising.
Published: 2013
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10. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Author: Fekadu Yadetie, Eric Westhof, Julie Poulain, Jean-Marc Aury, John H. Postlethwait, Claire Jubin, Scott William Roy, Atsuo Nishino, Matthieu Muffato, Lisbeth C. Olsen, Hiroki Nishida, Anke Konrad, Véronique Anthouard, Jean Weissenbach, Sutada Mungpakdee, Hugues Roest Crollius, Stephen Butcher, Corinne Da Silva, Evelyne Huynh Cong, Louis Du Pasquier, Helen Eikeseth-Otteraa, Jana Mikhaleva, Benjamin Noel, François Artiguenave, Marit Flo Jensen, Olivier Jaillon, David A. Liberles, Simon Henriet, Jean-Nicolas Volff, Henner Brinkmann, Sarabdeep Singh, Alexandra Louis, Pascal Chourrout, Coen Campsteijn, Marcin Adamski, Jean-Marie Bouquet, Cristian Cañestro, J. Robert Manak, Daniel Chourrout, Hervé Philippe, Gemma B. Danks, Hans Lehrach, Eric M. Thompson, Richard Reinhardt, Boris Lenhard, Snehalata Huzurbazar, Rym Kachouri-Lafond, Pierre Boudinot, Ismael Cross, Georgia Tsagkogeorga, Betina M. Porcel, Matteo Ugolini, Rein Aasland, Frédéric Delsuc, Patrick Wincker, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), SARS International Centre for Marine Molecular Biology, 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), Canadian Institute for Advanced Research (CIAR), Université de Montréal [Montréal], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Neuroscience, University of Oregon, Eugene, Oregon, University of Oregon [Eugene], Laboratorio de Genética, Universidad de Cádiz, Cádiz, Universidad de Cádiz (UCA), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), 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)-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), Department of Biology, University of Iowa, Iowa City, University of Iowa [Iowa City], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Biology, University of Wyoming, Laramie, University of Wyoming (UW), Department of Statistics, University of Wyoming, Laramie, Enseignement-Formation-Apprentissage (EFA), Université de Mons-Hainaut, 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, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, Osaka University, Osaka, Osaka University [Osaka], American Hospital of Paris, Hôpital Américain de Paris, University of Bergen (UIB), Department of Vertebrate Genomics [Berlin], Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, National Center for Biotechnology Information (NCBI), Institute of Neuroscience, University of Oregon, Eugene, Institute of Zoology and Evolutionary Biology, University of Basel (Unibas), Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-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)-École normale supérieure - Paris (ENS Paris)-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)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Canadian Institute for Advanced Research (CIFAR), 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)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), University of Bergen (UiB), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), NSF [IOS-0719577, DBI-0743374], 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, 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), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), 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), 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)-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)-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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0106 biological sciences, GENES, Lineage (evolution), Molecular Sequence Data, Chordate, 010603 evolutionary biology, 01 natural sciences, Genome, Synteny, Article, INTRON, 03 medical and health sciences, Genes, Duplicate, Gene Order, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Animals, 14. Life underwater, Urochordata, Gene, 030304 developmental biology, Genetics, Recombination, Genetic, 0303 health sciences, Multidisciplinary, COMPLEXITY, biology, Genes, Homeobox, Exons, biology.organism_classification, Biological Evolution, Invertebrates, OIKOPLEURA-DIOICA, Introns, Oikopleura, Sister group, Evolutionary biology, ORIGINS, Vertebrates, DNA Transposable Elements, Spliceosomes, Oikopleura dioica, DNA, Intergenic, CAENORHABDITIS-ELEGANS
Abstract: Ocean Dweller Sequenced The Tunicates, which include the solitary free-swimming larvaceans that are a major pelagic component of our oceans, are a basal lineage of the chordates. In order to investigate the major evolutionary transition represented by these organisms, Denoeud et al. (p. 1381 , published online 18 November) sequenced the genome of Oikopleura dioica , a chordate placed by phylogeny between vertebrates and amphioxus. Surprisingly, the genome showed little conservation in genome architecture when compared to the genomes of other animals. Furthermore, this highly compacted genome contained intron gains and losses, as well as species-specific gene duplications and losses that may be associated with development. Thus, contrary to popular belief, global similarities of genome architecture from sponges to humans are not essential for the preservation of ancestral morphologies.
Published: 2010
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11. Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni

Author: Goran Neshich, Guilherme Oliveira, Kleider Torres, Paula R. Kuser, Mariana Simoes, Adhemar Zerlotini, François Artiguenave, and Diana Bahia
Subjects: Models, Molecular, Single-nucleotide polymorphism, Myosins, Polymorphism, Single Nucleotide, Cathepsin B, Epitope, Article, Triosephosphate isomerase, Protein structure, parasitic diseases, Animals, Molecular Biology, Gene, Genes, Helminth, Cathepsin, Genetics, biology, Helminth Proteins, Schistosoma mansoni, biology.organism_classification, Fatty Acid Transport Proteins, Antigens, Helminth, Parasitology, Triose-Phosphate Isomerase
Abstract: Single nucleotide polymorphism (SNP) markers have been shown to be useful in genetic investigations of medically important parasites and their hosts. In this paper, we describe the prediction and validation of SNPs in ESTs of Schistosoma mansoni. We used 107,417 public sequences of S. mansoni and identified 15,614 high-quality candidate SNPs in 12,184 contigs. The presence of predicted SNPs was observed in well characterized antigens and vaccine candidates such as those coding for myosin; Sm14 and Sm23; cathepsin B and triosephosphate isomerase (TPI). Additionally, SNPs were experimentally validated for the cathepsin B. A comparative model of the S. mansoni cathepsin B was built for predicting the possible consequences of amino acid substitutions on the protein structure. An analysis of the substitutions indicated that the amino acids were mostly located on the surface of the molecule, and we found no evidence for a significant conformational change of the enzyme. However, at least one of the substitutions could result in a structural modification of an epitope.
Published: 2007

12. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

Author: Graziano Pesole, Benjamin Noel, François Artiguenave, Alberto Policriti, Federica Cattonaro, Alessandro Vezzi, Delphine Jublot, Valérie Laucou, Michel Gouyvenoux, Eléonore Durand, Didier Merdinoglu, Cristian Del Fabbro, Giorgio Valle, Isabelle Le Clainche, Michael Alaux, Irena Juman, Erica Mica, Béatrice Segurens, Alberto Casagrande, Claude Scarpelli, Massimo Delledonne, Gabriele Di Gaspero, Jean-Marc Aury, David S. Horner, Marco Moroldo, M. Enrico Pè, Philippe Hugueney, Mario Pezzotti, Michel Caboche, Anne-Françoise Adam-Blondon, Véronique Anthouard, Nicola Vitulo, Alain Lecharny, Alain Billault, Virginie Vico, Olivier Jaillon, Christian Clepet, Sébastien Aubourg, Michele Morgante, Jean Weissenbach, Patrick Wincker, Nathalie Choisne, Aurélie Canaguier, Corinne Dasilva, Edgardo Ugarte, Philippe Chatelet, Clémence Bruyère, Vincent Dumas, Sophie Paillard, Fabrice Legeai, Nicoletta Felice, Simone Scalabrin, G Malacrida, Julie Poulain, Francis Quetier, Claire Jubin, 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), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Dipartimento di Matematica e Informatica - Universita Udine (DIMI), Università degli Studi di Udine - University of Udine [Italie], 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), Dipartimento di Scienze Agrarie ed Ambientali - Universita Udine (DISA), CRIBI (CRIBI), Università degli Studi di Padova = University of Padua (Unipd), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano = University of Milan (UNIMI), Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Istituto Tecnologie Biomediche, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), 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), 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), Dipartimento Scientifico e Tecnologico (DST), Università degli studi di Verona = University of Verona (UNIVR), Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, VIGNA-CRA Initiative (VIGNA-CRA INITIATIVE), Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, 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), Universita degli Studi di Padova, Università degli Studi di Milano [Milano] (UNIMI), Università degli studi di Bari Aldo Moro (UNIBA), Consiglio Nazionale delle Ricerche [Roma] (CNR), University of Verona (UNIVR), 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), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Università degli studi di Milano [Milano], Università degli studi di Bari, 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), Università degli Studi di Verona, O., Jaillon, J., Aury, B., Noel, A., Policriti, C., Clepet, Casagrande, Alberto, N., Choisne, S., Aubourg, N., Vitulo, C., Jubin, A., Vezzi, F., Legeai, P., Hugueney, C., Dasilva, D., Horner, E., Mica, D., Jublot, J., Poulain, C., Bruyère, A., Billault, B., Seguren, M., Gouyvenoux, E., Ugarte, F., Cattonaro, V., Anthouard, V., Vico, C., DEL FABBRO, M., Alaux, G., DI GASPERO, V., Duma, N., Felice, S., Paillard, I., Juman, M., Moroldo, S., Scalabrin, A., Canaguier, I., LE CLAINCHE, G., Malacrida, E., Durand, G., Pesole, V., Laucou, P., Chatelet, D., Merdinoglu, M., Delledonne, M., Pezzotti, A., Lecharny, C., Scarpelli, F., Artiguenave, M. E., Pè, G., Valle, M., Morgante, M., Caboche, A., ADAM BLONDON, J., Weissenbach, F., Quétier, and P., Wincker
Subjects: 0106 biological sciences, genotype, Arabidopsis, POLYPLOIDY, adaptation, 01 natural sciences, Genome, RNA, Transfer, Gene duplication, plant genomics, plant genome evolution, Sequencing, Vitis, vitis vinifera, genome sequencing, 2. Zero hunger, Genetics, Plant evolution, 0303 health sciences, Multidisciplinary, food and beverages, Exons, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Paleopolyploidy, Populus, RNA, Plant, ARABIDOPSIS-THALIANA, DNA-SEQUENCE, GENE, DUPLICATION, MAP, IDENTIFICATION, EVOLUTION, DNA, Intergenic, vine, Genome, Plant, assembly, Bioinformatics, Molecular Sequence Data, Genomics, Biology, Genes, Plant, Monocotyledon, DNA sequencing, Evolution, Molecular, Polyploidy, 03 medical and health sciences, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, angiosperm, genome, 030304 developmental biology, Whole genome sequencing, fungi, Oryza, Sequence Analysis, DNA, 15. Life on land, chronology, Introns, grapevine, MicroRNAs, polyploidy, Karyotyping, vitis classification, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract: International audience; The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
Published: 2007
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13. Evidence for a dispersed Hox gene cluster in the platyhelminth parasite Schistosoma mansoni

Author: David A. Johnston, Wenjie Wu, Lee Murphy, Martin Adams, Raymond J. Pierce, Hirohisa Hirai, Eric Viscogliosi, Guillaume Balavoine, Al Ivens, Christophe Noël, François Artiguenave, J. Cornette, and Monique Capron
Subjects: Chromosomes, Artificial, Bacterial, Sequence analysis, Molecular Sequence Data, Gene Expression, Biology, Genome, Chromosome Walking, Sequence Analysis, Protein, Genetics, Primer walking, Animals, Ciona intestinalis, Amino Acid Sequence, Hox gene, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Genes, Helminth, Phylogeny, Homeodomain Proteins, Bacterial artificial chromosome, Life Cycle Stages, Reverse Transcriptase Polymerase Chain Reaction, Genes, Homeobox, Chromosome Mapping, Gene Expression Regulation, Developmental, Schistosoma mansoni, biology.organism_classification, Larva, Homeobox
Abstract: In most bilaterian organisms so far studied, Hox genes are organized in genomic clusters and determine development along the anteroposterior axis. It has been suggested that this clustering, together with spatial and temporal colinearity of gene expression, represents the ancestral condition. However, in organisms with derived modes of embryogenesis and lineage-dependent mechanisms for the determination of cell fate, temporal colinearity of expression can be lost and Hox cluster organization disrupted, as is the case for the ecdysozoans Drosophila melanogaster and Caenorhabditis elegans and the urochordates Ciona intestinalis and Oikopleura dioica. We sought to determine whether a lophotrochozoan, the platyhelminth parasite Schistosoma mansoni, possesses a conserved or disrupted Hox cluster. Using a polymerase chain reaction (PCR)-based strategy, we have cloned and characterized three novel S. mansoni genes encoding orthologues of Drosophila labial (SmHox 1), deformed (SmHox4), and abdominal A (SmHox8), as well as the full-length coding sequence of the previously described Smox1, which we identify as an orthologue of fushi tarazu. Quantitative reverse transcriptase-PCR showed that the four genes were expressed at all life-cycle stages but that levels of expression were differentially regulated. Phylogenetic analysis and the conservation of "parapeptide'' sequences ('"-terminal to the homeodomains of SmHox8 and Smox1 support the grouping of platyhelminths within the lophotrochozoan clade. However, Bacterial Artificial Chromosome (BAC) library screening followed by genome walking failed to reconstitute a cluster. The BAC clones containing Hox genes were sequenced. and in no case were other Hox genes found on the same clone. Moreover, the SmHox4 and SmHox8 genes contained single very large introns (>40 kbp) further indicating that the schistosome Hox cluster is highly extended. Localization of the Hox genes to chromosomes using fluorescence in situ hybridization showed that SinHox4 and SmHox8 are on the long arm of chromosome 4, whereas SmHox1 and Smox1 are on chromosome 3. In silico screening of the available genome sequences corroborated results of Southern blotting and BAC library screening that indicate that there are no paralogues of SmHox1, SmHox4, or SmHox8. The schistosome Hox cluster is therefore not duplicated, but is both dispersed and disintegrated in the genome.
Published: 2005

14. Genome sequence of the plant pathogen Ralstonia solanacearum

Author: Jean Weissenbach, Patricia Siguier, Marcel Salanoubat, Nathalie Choisne, J. C. Camus, M. Lavie, C. Claudel-Renard, Cedric Robert, Philippe Brottier, Patrick Wincker, Sophie Mangenot, A. Billault, François Artiguenave, Manuel Levy, Michael Chandler, M. Whalen, Christine Gaspin, Laurence Cattolico, Thomas Schiex, Stéphane Genin, Sébastien Cunnac, Christian Boucher, William Saurin, Annick Moisan, Jérôme Gouzy, Patricia Thebault, Matthieu Arlat, N. Demange, Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Polymères Biopolymères Surfaces (PBS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-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), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), 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)-Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Institut de Chimie du CNRS (INC)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-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)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut Normand de Chimie Moléculaire Médicinale et Macromoléculaire (INC3M), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), 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)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, MESH: Sequence Analysis, DNA, Molecular Sequence Data, MESH: Gram-Negative Aerobic Rods and Cocci, Genomics, MESH: Biological Evolution, Biology, MESH: Virulence, MESH: Genome, Bacterial, Genome, 03 medical and health sciences, RALSTONIA SOLANACEARUM, Bacterial Proteins, Solanum lycopersicum, MESH: Lycopersicon esculentum, Gene, MESH: Bacterial Proteins, 030304 developmental biology, Genomic organization, Genetics, Whole genome sequencing, 0303 health sciences, Ralstonia solanacearum, Multidisciplinary, MESH: Molecular Sequence Data, Virulence, 030306 microbiology, MESH: Genomics, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gram-Negative Aerobic Rods and Cocci, Mobile genetic elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract: 47 refs.; International audience; Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
Published: 2002
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15. Genomic exploration of the hemiascomycetous yeasts: 10. Kluyveromyces thermotolerans

Author: Patrick Wincker, Bernard Dujon, Gaëlle Blandin, Alain Malpertuy, Bertrand Llorente, and François Artiguenave
Subjects: Mitochondrial DNA, Nuclear gene, Databases, Factual, Speciation, Saccharomyces cerevisiae, Molecular Sequence Data, Biophysics, Synteny, Biochemistry, Genome, DNA, Mitochondrial, DNA, Ribosomal, Orphan, Fungal Proteins, Kluyveromyces, Ascomycota, RNA, Transfer, Structural Biology, Gene Order, Genetics, Amino Acid Sequence, Molecular Biology, Gene, biology, Sequence Homology, Amino Acid, Chromosome Mapping, Cell Biology, Ribosomal RNA, Genetic code, biology.organism_classification, Genetic Code, Chromosomes, Fungal, Genome, Fungal
Abstract: A genomic exploration of Kluyveromyces thermotolerans was performed by random sequence tag (RST) analysis. We sequenced 2653 RSTs corresponding to inserts sequenced from both ends. We performed a systematic comparison with a complete set of proteins from Saccharomyces cerevisiae, other completely sequenced genomes and SwissProt. We identified six mitochondrial genes and 1358–1496 nuclear genes by comparison with S. cerevisiae. In addition, 25 genes were identified by comparison with other organisms. This corresponds to about 24% of the estimated gene content of this organism. A lower level of conservation is observed with orthologues to genes of S. cerevisiae previously classified as orphans. Gene order was found to be conserved between S. cerevisiae and K. thermotolerans in 56.5% of studied cases.
Published: 2001

16. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes

Author: Elisabeth Bon, Jean Weissenbach, William Saurin, Patrick Wincker, Micheline Wésolowski-Louvel, Michel Termier, Claire Toffano-Nioche, Michel Aigle, Jacky de Montigny, Philippe Brottier, Bertrand Llorente, Andrée Lépingle, Claude Gaillardin, Alain Malpertuy, Pascal Durrens, Serge Casaregola, Jean-Luc Souciet, Monique Bolotin-Fukuhara, Serge Potier, Guillemette Duchateau-Nguyen, François Artiguenave, Odile Ozier-Kalogeropoulos, Fredj Tekaia, Bernard Dujon, Gaëlle Blandin, Cécile Neuvéglise, Laboratoire de Génétique Moléculaire et Cellulaire (INRA UMR216-URA1925), Institut National de la Recherche Agronomique (INRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-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), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie et génétique (UMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de génétique moléculaire et cellulaire, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Speciation, Biodiversity, MESH: Research Support, Non-U.S. Gov't, Biochemistry, MESH: Gene Amplification, MESH: Variation (Genetics), MESH: Yeast, Structural Biology, Yeasts, Gene cluster, MESH: Phylogeny, Phylogeny, Genetics, 0303 health sciences, biology, MESH: Genomics, MESH: Comparative Study, Genomics, MESH: Saccharomyces cerevisiae, Horizontal gene transfer, MESH: Fungal Proteins, Genes, Fungal, Saccharomyces cerevisiae, Biophysics, MESH: Ascomycota, MESH: Sequence Homology, Nucleic Acid, Fungal Proteins, 03 medical and health sciences, MESH: Software, Ascomycota, Species Specificity, Phylogenetics, Sequence Homology, Nucleic Acid, Gene family, MESH: Species Specificity, Molecular Biology, Gene, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, 030306 microbiology, Gene Amplification, Genetic Variation, Cell Biology, 15. Life on land, biology.organism_classification, Yeast, MESH: Genes, Fungal, Software, Pathway
Abstract: We explored the biological diversity of hemiascomycetous yeasts using a set of 22 000 newly identified genes in 13 species through BLASTX searches. Genes without clear homologue in Saccharomyces cerevisiae appeared to be conserved in several species, suggesting that they were recently lost by S. cerevisiae. They often identified well-known species-specific traits. Cases of gene acquisition through horizontal transfer appeared to occur very rarely if at all. All identified genes were ascribed to functional classes. Functional classes were differently represented among species. Species classification by functional clustering roughly paralleled rDNA phylogeny. Unequal distribution of rapidly evolving, ascomycete-specific, genes among species and functions was shown to contribute strongly to this clustering. A few cases of gene family amplification were documented, but no general correlation could be observed between functional differentiation of yeast species and variations of gene family sizes. Yeast biological diversity seems thus to result from limited species-specific gene losses or duplications, and for a large part from rapid evolution of genes and regulatory factors dedicated to specific functions.
Published: 2000
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17. Genomic exploration of the hemiascomycetous yeasts: 6. Saccharomyces exiguus

Author: François Artiguenave, Serge Casaregola, Patrick Wincker, Andrée Lépingle, Claude Gaillardin, Elisabeth Bon, Cécile Neuvéglise, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mitochondrial DNA, Genes, Fungal, Molecular Sequence Data, Saccharomyces cerevisiae, Gene Dosage, Biophysics, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Saccharomyces, 03 medical and health sciences, Ascomycota, Structural Biology, Gene Duplication, Gene Order, Genetics, Homologous chromosome, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Duplicated gene, biology, 030306 microbiology, Genomics, Cell Biology, biology.organism_classification, Open reading frame, genomic DNA, DNA Transposable Elements, Genome, Fungal, Sequence Alignment
Abstract: Random sequence tags were obtained from a genomic DNA library of Saccharomyces exiguus. The mitochondrial genome appeared to be at least 25.7 kb in size, with a different organization compared to Saccharomyces cerevisiae. An unusual putative 953 bp long terminal repeated element associated to Ty3 was found. A set of 1451 genes was identified homologous to S. cerevisiae open reading frames. Only five genes were identified outside the S. cerevisiae taxon, confirming that S. exiguus is phylogenetically closely related to S. cerevisiae. Unexpectedly, numerous duplicated genes were found whereas they are unique in S. cerevisiae. The sequences are deposited at EMBL under the accession numbers: AL407377–AL409955.
Published: 2000

18. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Author: Jean Weissenbach, William C. Nierman, Christopher D. Town, A Perez-Perez, R. Cooke, Brian J. Haas, Samir Kaul, T Kato, Claire Fujii, J Militscher, Mitsuyo Kohara, Steven L. Salzberg, A Conrad, Hans-Werner Mewes, D. Haase, M. Scharfe, S Bangert, Hean L. Koo, W. Ansorge, Laurence Cattolico, Patrick Wincker, Rama Maiti, Marcel Salanoubat, Erika Asamizu, Bénédicte Purnelle, Luke J. Tallon, M flores, Grace Pai, P Brottier, Kumi Idesawa, Richard Holland, P Sellers, J C Venter, S Nakayama, Michela D'Angelo, Holger Erfle, Berthold Fartmann, Ai Matsuno, Elena Casacuberta, Barbara Simionati, T Wada, R Wiedelmann, Amparo Monfort, Chiaki Kiyokawa, M. Rizzo, Jeremy Peterson, D. Vitale, Joan Climent, M. Schäfer, C Takeuchi, Gertrud Mannhaupt, Terrance Shea, P Navarro, Gerald Nyakatura, Pere Puigdomènech, R Mache, Leslie A. Grivell, S. van Aken, Paolo Zaccaria, Stephen Rudd, H. Voss, B Ottenwälder, Todd Creasy, J Reichelt, C Berger-Llauro, M Laudie, K Hornischer, H Drzonek, J P Alcaraz, Kai Lemcke, M Unseld, N Jordan, C Robert, Shusei Sato, T Kimura, S Müller-Auer, Naomi Nakazaki, W Saurin, Daphne Preuss, M. de Haan, J Jenkins, Francis Quetier, D Duchemin, Xiaoying Lin, Alberto Pallavicini, A Watanabe, Petra Brandt, Klaus F. X. Mayer, Heiko Schoof, M Yamada, Javier Terol, Satoshi Tabata, Benes, John Gill, François Artiguenave, Yoshie Kishida, Nathalie Choisne, O Schön, C. Gabel, E Wurmbach, Michael A. Rieger, Alessandro Vezzi, T Kaneko, T. H. Löhnert, Owen White, G Kauer, M Matsumoto, M. Fuchs, A Walts, G Nordsiek, Michel Delseny, Shigemi Sasamoto, H Kranz, Rosario Liguori, Yasukazu Nakamura, David Masuy, H. Blöcker, De Simone, Miho Yasuda, Tamara Feldblyum, B. Obermaier, Giorgio Valle, Manuel Pérez-Alonso, Sayaka Shinpo, Kumiko Kawashima, A Cottet, Anagnostis Argiriou, T Rooney, A.C. Maarse, Dongying Wu, C Collado, T. Utterback, Claire M. Fraser, M. D. Bargues, Stefano Toppo, Marc Boutry, Akiko Muraki, Salanoubat, M., Lemcke, K., Rieger, M., Ansorge, W., Unseld, M., Fartmann, B., Valle, G., Blocker, H., Perezalonso, M., Obermaier, B., Delseny, M., Boutry, M., Grivell, L. A., Mache, R., Puigdomenech, P., DE SIMONE, V., Choisne, N., Artiguenave, F., Robert, C., Brottier, P., Wincker, P., Cattolico, L., Weissenbach, J., Saurin, W., Quetier, F., Schafer, M., Mullerauer, S., Gabel, C., Fuchs, M., Benes, V., Wurmbach, E., Drzonek, H., Erfle, H., Jordan, N., Bangert, S., Wiedelmann, R., Kranz, H., Voss, H., Holland, R., Brandt, P., Nyakatura, G., Vezzi, A., D'Angelo, M., Pallavicini, Alberto, Toppo, S., Simionati, B., Conrad, A., Hornischer, K., Kauer, G., Lohnert, T. H., Nordsiek, G., Reichelt, J., Scharfe, M., Schon, O., Bargues, M., Terol, J., Climent, J., Navarro, P., Collado, C., Perezperez, A., Ottenwalder, B., Duchemin, D., Cooke, R., Laudie, M., Bergerllauro, C., Purnelle, B., Masuy, D., DE HAAN, M., Maarse, A. C., Alcaraz, J. P., Cottet, A., Casacuberta, E., Monfort, A., Argiriou, A., Flores, M., Liguori, R., Vitale, D., Mannhaupt, G., Haase, D., and Schoof, H.
Subjects: DNA, Plant, Sequence analysis, Arabidopsis, plant, Genome, Complete sequence, Gene Duplication, Centromere, Plant genomics, model organism, Humans, genomic structure, Gene, Plant Proteins, Genetics, Multidisciplinary, biology, Chromosome, Chromosome Mapping, Sequence Analysis, DNA, biology.organism_classification, genome sequencing, Chromosome 3, Genome, Plant
Abstract: Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
Published: 2000

19. Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii

Author: Patrick Wincker, Cécile Neuvéglise, Elisabeth Bon, Huu-Vang Nguyen, François Artiguenave, Claude Gaillardin, Andrée Lépingle, Serge Casaregola, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, Molecular Sequence Data, Saccharomyces cerevisiae, Biophysics, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Genome, Homology (biology), Fungal Proteins, 03 medical and health sciences, Ascomycota, RNA, Transfer, Structural Biology, Gene Duplication, Debaryomyces hansenii, Genetics, Non-conventional yeast, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ribosomal DNA, 0303 health sciences, biology, Contig, 030306 microbiology, Nuclear Proteins, Cell Biology, biology.organism_classification, Mitochondrial DNA, DNA Transposable Elements, Genome, Fungal
Abstract: By analyzing 2830 random sequence tags (RSTs), totalling 2.7 Mb, we explored the genome of the marine, osmo- and halotolerant yeast, Debaryomyces hansenii. A contig 29 kb in length harbors the entire mitochondrial genome. The genes encoding Cox1, Cox2, Cox3, Cob, Atp6, Atp8, Atp9, several subunits of the NADH dehydrogenase complex 1 and 11 tRNAs were unambiguously identified. An equivalent number of putative transposable elements compared to Saccharomyces cerevisiae were detected, the majority of which are more related to higher eukaryote copia elements. BLASTX comparisons of RSTs with databases revealed at least 1119 putative open reading frames with homology to S. cerevisiae and 49 to other genomes. Specific functions, including transport of metabolites, are clearly over-represented in D. hansenii compared to S. cerevisiae, consistent with the observed difference in physiology of the two species. The sequences have been deposited with EMBL under the accession numbers AL436045–AL438874.
Published: 2000

20. Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica

Author: François Artiguenave, Cécile Neuvéglise, Elisabeth Bon, Andrée Lépingle, Chantal Feynerol, Serge Casaregola, Claude Gaillardin, Patrick Wincker, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, Molecular Sequence Data, Saccharomyces cerevisiae, Biophysics, Functional classification, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Genome, Homology (biology), Fungal Proteins, 03 medical and health sciences, Structural Biology, Gene Duplication, Yeasts, Genetics, Molecular Biology, Gene, Non-conventional yeast, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Sequence Homology, Amino Acid, biology, 030306 microbiology, Yarrowia, Cell Biology, biology.organism_classification, Mitochondrial DNA, GENOMIQUE, Ion homeostasis, DNA Transposable Elements, Genome, Fungal
Abstract: A total of 4940 random sequence tags of the dimorphic yeast Yarrowia lipolytica , totalling 4.9 Mb, were analyzed. BLASTX comparisons revealed at least 1229 novel Y. lipolytica genes 1083 genes having homology with Saccharomyces cerevisiae genes and 146 with genes from various other genomes. This confirms the rapid sequence evolution assumed for Y. lipolytica . Functional analysis of newly discovered genes revealed that several enzymatic activities were increased compared to S. cerevisiae , in particular, transport activities, ion homeostasis, and various metabolism pathways. Most of the mitochondrial genes were identified in contigs spanning more than 47 kb. Matches to retrotransposons were observed, including a S. cerevisiae Ty3 and a LINE element. The sequences have been deposited with EMBL under the accession numbers AL409956 – AL414895 .
Published: 2000

21. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

Author: Betina M. Porcel, Patrick Wincker, Philippe Grellier, François Artiguenave, Sébastien Charneau, Eric Maréchal, Isabelle Florent, Laurent Brehelin, Corinne Da Silva, Elodie Guillaume, Olivier Gascuel, Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: alignement de séquences, Genes, Protozoan, Protozoan Proteins, polymorphisme, Genome, polymorphism, Genomic library, Genetics, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, expression protein, 030302 biochemistry & molecular biology, Exons, Subtelomere, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], protéine, parasite, Bio-informatique, DNA microarray, RNA, Protozoan, Biotechnology, Research Article, lcsh:QH426-470, Bioinformatics, lcsh:Biotechnology, Molecular Sequence Data, Plasmodium falciparum, Schizonts, Biology, 03 medical and health sciences, lcsh:TP248.13-248.65, parasitic diseases, gene, genome, Human parasite, sequence alignment, Apicomplexa, Animals, Gene, 030304 developmental biology, Gene Library, Polymorphism, Genetic, Models, Genetic, génome, Intron, Sequence Analysis, DNA, Actin cytoskeleton, Introns, lcsh:Genetics, structure génétique, RNA, Ribosomal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Protozoan, Sequence Alignment
Abstract: Background The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and functional assessments of P. falciparum genes and expression, and polymorphic data are further necessary to exploit genomic information to further qualify therapeutic target candidates. Here, we undertook a large scale analysis of a P. falciparum FcB1-schizont-EST library previously constructed by suppression subtractive hybridization (SSH) to study genes expressed during merozoite morphogenesis, with the aim of: 1) obtaining an exhaustive collection of schizont specific ESTs, 2) experimentally validating or correcting P. falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains. Results A total of 22,125 clones randomly picked from the SSH library were sequenced, yielding 21,805 usable ESTs that were then clustered on the P. falciparum genome. This allowed identification of 243 protein coding genes, including 121 previously annotated as hypothetical. Statistical analysis of GO terms, when available, indicated significant enrichment in genes involved in "entry into host-cells" and "actin cytoskeleton". Although most ESTs do not span full-length gene reading frames, detailed sequence comparison of FcB1-ESTs versus 3D7 genomic sequences allowed the confirmation of exon/intron boundaries in 29 genes, the detection of new boundaries in 14 genes and identification of protein polymorphism for 21 genes. In addition, a large number of non-protein coding ESTs were identified, mainly matching with the two A-type rRNA units (on chromosomes 5 and 7) and to a lower extent, two atypical rRNA loci (on chromosomes 1 and 8), TARE subtelomeric regions (several chromosomes) and the recently described telomerase RNA gene (chromosome 9). Conclusion This FcB1-schizont-EST analysis confirmed the actual expression of 243 protein coding genes, allowing the correction of structural annotations for a quarter of these sequences. In addition, this analysis demonstrated the actual transcription of several remarkable non-protein coding loci: 2 atypical rRNA, TARE region and telomerase RNA gene. Together with other collections of P. falciparum ESTs, usually generated from mixed parasite stages, this collection of FcB1-schizont-ESTs provides valuable data to gain further insight into the P. falciparum gene structure, polymorphism and expression.
Published: 2009
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22. Annotating genomes with massive-scale RNA sequencing

Author: Patrick Wincker, François Artiguenave, Claude Scarpelli, Jean-Marc Aury, Odile Rogier, Giorgio Valle, Olivier Jaillon, Michele Morgante, Benjamin Noel, Corinne Da Silva, Massimo Delledonne, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Verona (UNIVR), Istituto di Genomica Applicata, Universita di Padova, Università degli studi di Verona = University of Verona (UNIVR), and Università degli Studi di Padova = University of Padua (Unipd)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, DNA, Complementary, Sequence analysis, genetic processes, Method, Genomics, Biotechnologies, annotation génomique, Computational biology, Biology, 01 natural sciences, Genome, 03 medical and health sciences, natural sciences, Vitis, Gene, 030304 developmental biology, Comparative genomics, Genetics, 0303 health sciences, Models, Genetic, Sequence Analysis, RNA, Annotating genomes with massive-scale RNA sequencing, séquençage nouvelle génération, ComputingMethodologies_PATTERNRECOGNITION, RNA, Plant, RNA splicing, séquençage adn, Functional genomics, Genome, Plant, 010606 plant biology & botany, Personal genomics
Abstract: A method for de novo genome annotation using high-throughput cDNA sequencing data., Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome.
Published: 2008
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23. Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

Author: Patrick Wincker, François Artiguenave, Andrée Lépingle, Serge Casaregola, Elisabeth Bon, Claude Gaillardin, Cécile Neuvéglise, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: tRNA gene, Molecular Sequence Data, Saccharomyces cerevisiae, Karyotype, Biophysics, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Fungal Proteins, Open Reading Frames, Saccharomyces, 03 medical and health sciences, chemistry.chemical_compound, Ascomycota, RNA, Transfer, Structural Biology, Genetics, Melibiose, Molecular Biology, Gene, Ribosomal DNA, ComputingMilieux_MISCELLANEOUS, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Cell Biology, biology.organism_classification, Long terminal repeat, Yeast, Open reading frame, chemistry, 13. Climate action, Genome, Fungal
Abstract: The genome of Saccharomyces kluyveri was explored through 2528 random sequence tags with an average length of 981 bp. The complete nuclear ribosomal DNA unit was found to be 8656 bp in length. Sequences homologous to retroelements of the gypsy and copia types were identified as well as numerous solo long terminal repeats. We identified at least 1406 genes homologous to Saccharomyces cerevisiae open reading frames, with on average 58.1% and 72.4% amino acid identity and similarity, respectively. In addition, by comparison with completely sequenced genomes and the SwissProt database, we found 27 novel S. kluyveri genes. Most of these genes belong to pathways or have functions absent from S. cerevisiae , such as the catabolic pathway of purines or pyrimidines, melibiose fermentation, sorbitol utilization, or degradation of pollutants. The sequences are deposited in EMBL under the accession numbers AL404849 – AL407376 .
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24. Genomic Exploration of the Hemiascomycetous Yeasts: 13. Pichia angusta

Author: Bertrand Llorente, Bernard Dujon, Alain Malpertuy, Patrick Wincker, François Artiguenave, and Gaëlle Blandin
Subjects: DNA Replication, Mitochondrial DNA, Saccharomyces cerevisiae, Molecular Sequence Data, Intron, Biophysics, Retrotransposon, Biochemistry, Genome, DNA, Mitochondrial, DNA, Ribosomal, Pichia, Fungal Proteins, Ascomycota, RNA, Transfer, Structural Biology, Genetics, Genomic library, Molecular Biology, Gene, Ribosomal DNA, Comparative genomics, biology, Cell Biology, biology.organism_classification, Introns, Multigene Family, DNA Transposable Elements, Spliceosomes, Genome, Fungal, Plasmids
Abstract: As part of a comparative genomics project on 13 hemiascomycetous yeasts, the Pichia angusta type strain was studied using a partial random sequencing strategy. With coverage of 0.5 genome equivalents, about 2500 novel protein-coding genes were identified, probably corresponding to more than half of the P. angusta protein-coding genes, 6% of which do not have homologs in Saccharomyces cerevisiae. Some of them contain one or two introns, on average three times shorter than those in S. cerevisiae. We also identified 28 tRNA genes, a few retrotransposons similar to Ty5 of S. cerevisiae, solo long terminal repeats, the whole ribosomal DNA cluster, and segments of mitochondrial DNA. The P. angusta sequences were deposited in EMBL under the accession numbers AL430961 to AL436044.
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25. Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

Author: Claire Toffano-Nioche, Bertrand Llorente, Andrée Lépingle, Jacky de Montigny, Philippe Brottier, Elisabeth Bon, François Artiguenave, Bernard Dujon, Jean-Luc Souciet, Gaëlle Blandin, Alain Malpertuy, William Saurin, Pascal Durrens, Cécile Neuvéglise, Micheline Wésolowski-Louvel, Serge Potier, Claude Gaillardin, Serge Casaregola, Odile Ozier-Kalogeropoulos, Michel Aigle, Monique Bolotin-Fukuhara, Fredj Tekaia, Patrick Wincker, and Jean Weissenbach
Subjects: Maverick, Novel gene, Saccharomyces cerevisiae, Genes, Fungal, Biophysics, Questionable open reading frame, Biochemistry, Genome, Evolution, Molecular, Orphan, Ascomycota, Species Specificity, Structural Biology, Sequence comparison, Genetics, Gene number, ORFS, Molecular Biology, Gene, Conserved Sequence, biology, Base Sequence, Phylum, Genetic Variation, Cell Biology, biology.organism_classification, Yeast, Open reading frame
Abstract: Comparisons of the 6213 predicted Saccharomyces cerevisiae open reading frame (ORF) products with sequences from organisms of other biological phyla differentiate genes commonly conserved in evolution from ‘maverick’ genes which have no homologue in phyla other than the Ascomycetes. We show that a majority of the ‘maverick’ genes have homologues among other yeast species and thus define a set of 1892 genes that, from sequence comparisons, appear ‘Ascomycetes-specific’. We estimate, retrospectively, that the S. cerevisiae genome contains 5651 actual protein-coding genes, 50 of which were identified for the first time in this work, and that the present public databases contain 612 predicted ORFs that are not real genes. Interestingly, the sequences of the ‘Ascomycetes-specific’ genes tend to diverge more rapidly in evolution than that of other genes. Half of the ‘Ascomycetes-specific’ genes are functionally characterized in S. cerevisiae, and a few functional categories are over-represented in them.
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26. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

Author: William Saurin, Cécile Neuvéglise, Bertrand Llorente, Philippe Brottier, Andrée Lépingle, Bernard Dujon, Micheline Wésolowski-Louvel, Serge Casaregola, Monique Bolotin-Fukuhara, Claire Toffano-Nioche, Gaëlle Blandin, Elisabeth Bon, Odile Ozier-Kalogeropoulos, Patrick Wincker, Jean Weissenbach, Alain Malpertuy, François Artiguenave, Pascal Durrens, Michel Aigle, Serge Potier, Claude Gaillardin, Jean-Luc Souciet, Fredj Tekaia, Jacky de Montigny, Microbiologie et Génétique Moléculaire (MGM), and Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, Gene duplication, Genes, Fungal, Saccharomyces cerevisiae, Biophysics, Gene redundancy, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Evolution, Molecular, 03 medical and health sciences, Ascomycota, Structural Biology, Gene cluster, Genetics, Gene family, Molecular Biology, Gene, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Base Sequence, Models, Genetic, biology, Gene deletion, 030302 biochemistry & molecular biology, Genetic Variation, Cell Biology, Telomere, biology.organism_classification, Paralogue, Multigene Family, Orthologue, Genome, Fungal
Abstract: We have evaluated the degree of gene redundancy in the nuclear genomes of 13 hemiascomycetous yeast species. Saccharomyces cerevisiae singletons and gene families appear generally conserved in these species as singletons and families of similar size, respectively. Variations of the number of homologues with respect to that expected affect from 7 to less than 24% of each genome. Since S. cerevisiae homologues represent the majority of the genes identified in the genomes studied, the overall degree of gene redundancy seems conserved across all species. This is best explained by a dynamic equilibrium resulting from numerous events of gene duplication and deletion rather than by a massive duplication event occurring in some lineages and not in others.
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27. Genomic Exploration of the Hemiascomycetous Yeasts: 15. Pichia sorbitophila

Author: Patrick Wincker, Catherine Spehner, Jacky de Montigny, Fredj Tekaia, Bernard Dujon, Serge Potier, Jean-Luc Souciet, and François Artiguenave
Subjects: Homothallism, Nuclear gene, Molecular Sequence Data, Saccharomyces cerevisiae, Biophysics, Locus (genetics), DNA, Mitochondrial, DNA, Ribosomal, Biochemistry, Pichia, Fungal Proteins, Ascomycota, RNA, Transfer, Structural Biology, Genetics, Molecular Biology, Gene, Phylogeny, Random sequence tag, Comparative genomics, Fungal protein, Sequence Homology, Amino Acid, biology, Nuclear Proteins, Sequence Analysis, DNA, Cell Biology, biology.organism_classification, DNA Transposable Elements, Hemiascomycete, Genome, Fungal
Abstract: This paper reports the genomic analysis of the strain CBS7064 of Pichia sorbitophila, a homothallic diploid yeast. We sequenced 4829 random sequence tags of about 1 kb and compared them to the Saccharomyces cerevisiae gene products. Approximately 1300 nuclear genes, 22 tRNAs, the rDNA locus, and six mitochondrial genes have been identified. The analysis of the rDNA genes has permitted to classify this organism close to the Candida species. Accession numbers from AL414896 to AL419724 at EMBL databank.
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27 results on '"François Artiguenave"'

1. Genomic Investigation of Balanced Chromosomal Rearrangements in Patients with Abnormal Phenotypes

2. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

3. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

4. Genomic Exploration of the Hemiascomycetous Yeasts: 12. Kluyveromyces marxianus var. marxianus

5. Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae

6. Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies1

7. Genomic Exploration of the Hemiascomycetous Yeasts: 11.Kluyveromyces lactis

8. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

9. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining

10. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

11. Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni

12. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

13. Evidence for a dispersed Hox gene cluster in the platyhelminth parasite Schistosoma mansoni

14. Genome sequence of the plant pathogen Ralstonia solanacearum

15. Genomic exploration of the hemiascomycetous yeasts: 10. Kluyveromyces thermotolerans

16. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes

17. Genomic exploration of the hemiascomycetous yeasts: 6. Saccharomyces exiguus

18. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

19. Genomic exploration of the hemiascomycetous yeasts: 14. Debaryomyces hansenii var. hansenii

20. Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica

21. A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

22. Annotating genomes with massive-scale RNA sequencing

23. Genomic Exploration of the Hemiascomycetous Yeasts: 9. Saccharomyces kluyveri

24. Genomic Exploration of the Hemiascomycetous Yeasts: 13. Pichia angusta

25. Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

26. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

27. Genomic Exploration of the Hemiascomycetous Yeasts: 15. Pichia sorbitophila

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