Search

Your search keyword '"Simone Duprat"' showing total 14 results
Start Over Author "Simone Duprat"
14 results on '"Simone Duprat"'

1. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

Published
2024
Full Text
View/download PDF

2. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Published
2024
Full Text
View/download PDF

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
Full Text
View/download PDF

4. Molecular analysis of nonrandom 8q12 deletions in acute lymphoblastic leukemia: Identification of two candidate genes

Author

Isabelle Devaux, Gilles Hetet, Laetitia Gressin, Etienne Vilmer, Nathalie Couque, Laurence Cattolico, Simone Duprat, Hélène Cavé, Valérie Bardet, and Bernard Grandchamp

Subjects
Genetics, Untranslated region, Cancer Research, Exon, Candidate gene, Bacterial artificial chromosome, Tumor suppressor gene, Putative gene, Biology, Gene, Molecular biology, GC-content
Abstract

Acute lymphoblastic leukemia is the most common malignancy in childhood. High-resolution allelotyping performed in our laboratory showed new chromosomal sites of nonrandom deletions. We have focused our work on 8q12 deletions, which we have found in about 4% of patients (eight of 205 informative cases). These deletions were of small size (less than 1 Mb) in all but one patient, and the deleted region common to all patients was delineated between two microsatellite markers (D8S1113 and D8S1763). This region was sequenced entirely from two overlapping bacterial artificial chromosomes. The common deleted region (120 kb) had a low GC content (37%), was composed more than 50% of LINE sequences, and contained only two candidate genes. The centromeric deletion borders were clustered within an interval of 33 kb between two microsatellite markers. This interval contains the first exon of an HMG-1-related gene (KIAA0808) and a putative gene, DL8q12, predicted to encode a protein with 231 amino acid residues with no homolog in protein databases. Analysis of the available mRNA from lymphoblastic cells of two patients with 8q12 deletions using common polymorphisms in the 3′ UTR of KIAA0808 showed monoallelic expression of this gene. Identification of a biallelic polymorphism in the first exon of DL8q12 showed that this gene was deleted in two of four informative cases. Sequencing of the exons of both genes from all patients with 8q12 deletions did not show any mutation, which suggests that neither of these genes behaves as a classic tumor suppressor gene. © 2002 Wiley-Liss, Inc.

Published
2001
Full Text
View/download PDF

5. Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea

Author

Odile Lecompte, Valérie Puzos-Barbe, Raymond Ripp, Roland Heilig, Jean-Claude Thierry, Simone Duprat, Jacques Dietrich, Olivier Poch, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
Genome evolution, Letter, Hot Temperature, Pyrococcus, Proteome, Chromosomes, Archaeal, Archaeal Proteins, Molecular Sequence Data, Biology, Genome, Genes, Archaeal, Evolution, Molecular, Species Specificity, Genome, Archaeal, Molecular evolution, Phylogenetics, Sequence Homology, Nucleic Acid, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, Genetics (clinical), [SDV.GEN]Life Sciences [q-bio]/Genetics, Phylogenetic tree, Gene Amplification, Genome project, Pyrococcus furiosus, Evolutionary biology, Horizontal gene transfer, Chromosome Deletion
Abstract

The complete genome projects span the major branches of the archaeal and eubacterial phylogenetic trees and many eukaryotic genomes will be soon available. This genomic revolution has provided a considerable amount of data and enables comparative studies between distant organisms at the comprehensive and integrative level of genomes. They have revealed a remarkable genomic plasticity because dynamic rearrangements occurred so frequently, not only at large evolutionary distances but also between related species such as Escherichia coli and Haemophilus influenza, that gene order conservation is restricted to a few operons (Koonin and Galperin 1997; Siefert et al. 1997; Smith et al. 1997; Watanabe et al. 1997; de Rosa and Labedan 1998). Genomic comparisons have also highlighted the high variability of gene content, leading to a very small set of universal proteins mainly restricted to informational families (proteins involved in replication, transcription, and translation) (Huynen and Bork 1998; Kyrpides et al. 1999; Koonin et al. 2000). This underlines the considerable plasticity in biochemical pathways, with several solutions being independently invented in the course of evolution to achieve essential functions. Even at smaller evolutionary intervals, many individual genes show tree topologies in fundamental disagreement with the organismal phylogeny. Such mosaic phylogenies have revealed the unforeseen importance of lineage-specific losses and acquisition by horizontal transfer in the course of evolution. The relative extent of horizontal gene transfer versus lineage-specific gene losses has been hotly debated, in particular between Eubacteria and Archaea (Aravind et al. 1998; Kyrpides and Olsen 1999). The importance of DNA exchange between very distant prokaryotes belonging to distinct domains questions the commonly accepted scenario of the emergence of life and the universal phylogenetic tree (Koonin et al. 1997; Gupta 1998; Forterre and Philippe 1999). Nevertheless, all of these studies have emphasized that identification of truly orthologous relationships between genomes is a prerequisite to performing confident comparative genomic analysis. In fact, orthologous genes evolved from a common ancestral gene by speciation, whereas paralogous genes resulted from a duplication event (Fitch 1970). However, intricate relationships are hidden behind these definitions and the identification of true orthologs is not trivial in practice. As a consequence, the interpretation of genomic comparisons between distant lineages is a challenging task. Comparisons of closely related species constitute a complementary approach crucial to the understanding of the forces at work in genome evolution. At the genomic level, they provide a unique opportunity to understand the mechanisms that determine chromosomal organization and evolution. At the proteomic level, this is a powerful strategy to assess the genuine extent of gene losses and gains that lead to the observed divergence of coding capacity. Until now, within- and between-species comparisons have been performed only on pathogenic Eubacteria (Himmelreich et al. 1997; Herrmann and Reiner 1998; Alm et al. 1999; Kalman et al. 1999; Read et al. 2000). They provided new insights into molecular evolution at the genome scale in Eubacteria and permitted the correlation of specific genes with phenotypic properties. In contrast, little is known about the evolution of closely related archaeal genomes, which are of particular interest because they show an eubacterial form with an eukaryotic content (Keeling et al. 1994). Indeed, most of the proteins involved in cell division or in metabolic pathways are eubacterial-like, whereas the informational genes are eukaryotic-like (Brown and Doolittle 1997; Koonin and Galperin 1997; Doolittle and Logsdon 1998). Here we present the detailed genome-scale comparison of three closely related species of free-living Archaea: Pyrococcus abyssi, Pyrococcus horikoshii (Kawarabayasi et al. 1998), and Pyrococcus furiosus (Maeder et al. 1999). This was made possible by the recent sequencing of P. abyssi whose annotations and phylogenetic relationships with nonpyrococcal species will be discussed elsewhere (O. Poch, in prep.). The three species are hyperthermophilic Euryarchaea belonging to the Thermococcales order (Fiala and Stetter 1986; Erauso et al. 1993; Gonzalez et al. 1998). We have compared these three genomes at different levels: chromosomal organization, evolutionary distances, and gene content.

Published
2001
Full Text
View/download PDF

6. Sequence and Analysis of Chromosome I of the Amitochondriate Intracellular Parasite Encephalitozoon cuniculi (Microspora)

Author

Simone Duprat, Valérie Barbe, Michael Katinka, Christian P. Vivarès, Martin Barbazanges, William Saurin, Pierre Peyret, Jean Weissenbach, and Francis Duffieux

Subjects
Intracellular Fluid, Sequence analysis, Genes, Protozoan, Molecular Sequence Data, Biology, Genome, Open Reading Frames, chemistry.chemical_compound, Gene Order, Genetics, Animals, Gene, Encephalitozoon cuniculi, Dyad symmetry, Genetics (clinical), Base Composition, Intron, Chromosome Mapping, Sequence Analysis, DNA, DNA, Protozoan, Telomere, biology.organism_classification, Open reading frame, chemistry, Tandem Repeat Sequences, DNA, Reports
Abstract

A DNA sequencing program was applied to the small (Encephalitozoon cuniculi, an amitochondriate eukaryotic parasite of mammals, and the sequence of the smallest chromosome was determined. The ∼224-kb E. cuniculichromosome I exhibits a dyad symmetry characterized by two identical 37-kb subtelomeric regions which are divergently oriented and extend just downstream of the inverted copies of an 8-kb duplicated cluster of six genes. Each subtelomeric region comprises a single 16S–23S rDNA transcription unit, flanked by various tandemly repeated sequences, and ends with ∼1 kb of heterogeneous telomeric repeats. The central (or core) region of the chromosome harbors a highly compact arrangement of 132 potential protein-coding genes plus two tRNA genes (one gene per 1.14 kb). Most genes occur as single copies with no identified introns. Of these putative genes, only 53 could be assigned to known functions. A number of genes from the transcription and translation machineries as well as from other cellular processes display characteristic eukaryotic signatures or are clearly eukaryote-specific.[The sequence data described in this paper have been submitted to the EMBL data library under accession no. AL 391737.]

Published
2001
Full Text
View/download PDF

7. Genomic Exploration of the Hemiascomycetous Yeasts: 2. Data generation and processing

Author

Simone Duprat, William Saurin, Claude Scarpelli, Patrick Wincker, François Artiguenave, Jean Weissenbach, Phillippe Brottier, Virginie Vico, Jean Verdier, and Fabien Jovelin

Subjects
Genetics, High-throughput sequencing, Genome, Sequence analysis, Test data generation, Sequencing data, Biophysics, Computational Biology, Sequence Analysis, DNA, Cell Biology, Computational biology, Biology, Biochemistry, Pichia, DNA sequencing, DNA sequencer, Ascomycota, Structural Biology, Hemiascomycete, Genome, Fungal, Molecular Biology, Reaction tube
Abstract

The generation of sequencing data for the hemiascomycetous yeast random sequence tag project was performed using the procedures established at GENOSCOPE. These procedures include a series of protocols for the sequencing reactions, using infra-red labelled primers, performed on both ends of the plasmid inserts in the same reaction tube, and their analysis on automated DNA sequencers. They also include a package of computer programs aimed at detecting potential assignation errors, selecting good quality sequences and estimating their useful length.

Published
2000
Full Text
View/download PDF

8. A Gene Map of the Human Genome

Author

Christopher Mader, B. B. Birren, Jean Morissette, C. Sanders, K. Swanson, Xiao-Yu Wu, Thomas J. Hudson, Mark S. Boguski, A. Maratukulam, Midori A. Harris, L. Green, S. Hussain, C. East, Robert E. White, Andrew A. Hicks, K. R. Iorio, Andrew B. Castle, W.-L. Sun, Paul Harrison, Simone Duprat, Kate Rice, Eric S. Lander, X. She, Shanti M. Perkins, Ammon B. Peck, Mina Sandusky, John Quackenbush, L. Hui, David Bentley, K. B. McKusick, Anindya Dehejia, Gregory D. Schuler, Gabor Gyapay, T. Dibling, C M Clee, Amita Aggarwal, James R. Hudson, R. Torres, Eva Bajorek, Peter N. Goodfellow, Mark Piercy, Mark Raymond Adams, Jun Fan, Cheryl Phillips, Elizabeth A. Stewart, Nicole Y. Fang, N. Drouot, Ian Dunham, Donna K. Slonim, Mihael H. Polymeropoulos, N. Nomura, Andrew J. Mungall, K. Ishikawa, E. Holloway, J. Ma, P. J. R. Day, N. Seki, S. Bentolila, Jean Weissenbach, P. Rodriguez-Tomé, Adam Butler, Sid Cowles, Angela M. Chu, Karin Schmitt, R. Houlgatte, Panos Deloukas, Tim Reif, Michael R. James, C. Louis-Dit-Sully, S. Voyticky, P. Tabar, David R. Cox, A. MacGilvery, David C. Page, Carol Soderlund, C A Edwards, S A Ranby, Nicole A.R. Walter, Douglas Vollrath, T. E. Wilmer, Lincoln Stein, H. C. Nusbaum, Takahiro Nagase, Tara C. Matise, T. Thangarajah, Susan E. Ide, Fawn Qin, Richard M. Myers, Steve Rozen, Jacques S. Beckmann, Richard Berry, James M. Sikela, Charles Auffray, Shannon T. Brady, Cécile Fizames, Christine Garrett, David Hadley, Delphine Muselet, Nathalie Vega-Czarny, Rhonda Brandon, Wha‐Young Lee, N. Chiannilkulchai, J. C. Venter, and James Silva

Subjects
Sequence-tagged site, Yeast artificial chromosome, Genetics, Expressed sequence tag, Multidisciplinary, Gene map, Gene mapping, Human genome, Computational biology, Genome project, Biology, Genome
Abstract

The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.

Published
1996
Full Text
View/download PDF

9. Annotation of microsporidian genomes using transcriptional signals

Author

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

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

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

Published
2012
Full Text
View/download PDF

10. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

Author

Philippe Marlière, Catherine Robert, Sophie Oztas, Stéphane Cruveiller, Patrick Wincker, David Vallenet, Claudine Médigue, L. Nicholas Ornston, Nuria Fonknechten, Jean Weissenbach, Laurent Labarre, Georges N. Cohen, Simone Duprat, Annett Kreimeyer, and Valérie Barbe

Subjects
Molecular Sequence Data, Coenzymes, Genome, Synteny, Evolution, Molecular, Polysaccharides, Nucleic Acids, Genetics, Amino Acids, Gene, Nitrites, Whole genome sequencing, Nitrates, biology, Acinetobacter, Base Sequence, Sulfates, Circular bacterial chromosome, Pseudomonas, Biological Transport, Articles, Vitamins, biology.organism_classification, Pseudomonas putida, Aerobiosis, Transformation, Bacterial, Energy Metabolism, GC-content, Genome, Bacterial
Abstract

Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome

Published
2004

11. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Author

Nicole Stange-Thomann, Michael Katinka, Michael Levy, Vincent Laudet, Olivier Jaillon, Cécile Fischer, Véronique de Berardinis, Zineb Skalli, Jill P. Mesirov, David M. Jaffe, Alain Bernot, Genís Parra, Simone Duprat, Claude Scarpelli, Daniel Kahn, Chad Nusbaum, Sophie Nicaud, Laurence Bouneau, Francis Quetier, Hugues Roest Crollius, Corinne Cruaud, Bruce W. Birren, Jérôme Gouzy, Kevin McKernan, Eric S. Lander, Nathalie Boudet, Vanina Castelli, Marc Robinson-Rechavi, Jean-Pierre Coutanceau, Béatrice Segurens, Michael C. Zody, Corinne Dasilva, Evan Mauceli, Paul A. McEwan, Manolis Kellis, Carole Dossat, Benoit Vacherie, Marcel Salanoubat, Roderic Guigó, Sheila Fisher, Christian Biémont, Stephanie Bosak, Jean Weissenbach, Véronique Anthouard, Jean-Nicolas Volff, William Saurin, Vincent Schächter, Julie Poulain, Catherine Ozouf-Costaz, Jean-Louis Petit, Laurence Cattolico, Guillaume Lardier, Charles Chapple, Sergi Castellano, Georges Lutfalla, Frédéric Brunet, Kerstin Lindblad-Toh, Philippe Brottier, Claire Jubin, Patrick Wincker, Jean-Marc Aury, Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), 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)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), 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), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), 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), Unité mixte de recherche biologie moléculaire de la cellule, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Department of Atmospheric and Environmental Chemistry [Bothell], University of Washington-Bothell, Bayer Cropscience, Centre d'étude spatiale des rayonnements (CESR), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
Genome evolution, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Proteome, [SDV]Life Sciences [q-bio], Molecular Sequence Data, 2R hypothesis, Tetraodon nigroviridis, Fish Proteins, Synteny, Genome, Chromosomes, Evolution, Molecular, Gene Duplication, biology.animal, Animals, Chromosomes, Human, Humans, Urochordata, Tetraodon, Conserved Sequence, Mammals, Genetics, Base Composition, Multidisciplinary, Models, Genetic, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Fishes, Vertebrate, Sequence Analysis, DNA, Physical Chromosome Mapping, biology.organism_classification, Genes, Karyotyping, Vertebrates, Human genome
Abstract

International audience; Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Published
2004
Full Text
View/download PDF

12. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing

Author

Laurence Cattolico, Sébastien Kicka, Béatrice Turcq, Simone Duprat, Christian Barreau, Robert Debuchy, Philippe Silar, Jean Weissenbach, Carole H. Sellem, Alain Billault, Annie Sainsard-Chanet, and Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Sordariales, MESH: Sequence Analysis, DNA, Chromosomes, Artificial, Bacterial, MESH: Introns, Sordariales, Sequence Homology, MESH: Amino Acid Sequence, Genome, Podospora anserina, RNA, Transfer, MESH: Sequence Homology, Genomic organization, Genetics, Gene Rearrangement, 0303 health sciences, Genomic Library, biology, 030302 biochemistry & molecular biology, MESH: Genomic Library, MESH: Synteny, Physical Chromosome Mapping, MESH: Chromosomes, Fungal, MESH: Genome, Fungal, MESH: Centromere, DNA, Intergenic, Chromosomes, Fungal, Genome, Fungal, MESH: Chromosomes, Artificial, Bacterial, MESH: Gene Rearrangement, Centromere, Genes, Fungal, Molecular Sequence Data, MESH: Physical Chromosome Mapping, Microbiology, Synteny, 03 medical and health sciences, Gene density, MESH: Genes, rRNA, Amino Acid Sequence, Gene, 030304 developmental biology, MESH: DNA, Intergenic, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Molecular Sequence Data, Chromosome, Genes, rRNA, Sequence Analysis, DNA, MESH: RNA, Transfer, biology.organism_classification, Introns, MESH: Genes, Fungal
Abstract

International audience; A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.

Published
2003
Full Text
View/download PDF

13. Molecular analysis of nonrandom 8q12 deletions in acute lymphoblastic leukemia: identification of two candidate genes

Author

Valérie, Bardet, Nathalie, Couque, Laurence, Cattolico, Gilles, Hetet, Isabelle, Devaux, Simone, Duprat, Laetitia, Gressin, Etienne, Vilmer, Hélène, Cavé, and Bernard, Grandchamp

Subjects
Male, Adolescent, Molecular Sequence Data, Infant, Sequence Analysis, DNA, Burkitt Lymphoma, Child, Preschool, Humans, Female, Gene Silencing, Chromosome Deletion, Cloning, Molecular, Child, Alleles, Chromosomes, Human, Pair 8, Genes, Neoplasm, Sequence Deletion
Abstract

Acute lymphoblastic leukemia is the most common malignancy in childhood. High-resolution allelotyping performed in our laboratory showed new chromosomal sites of nonrandom deletions. We have focused our work on 8q12 deletions, which we have found in about 4% of patients (eight of 205 informative cases). These deletions were of small size (less than 1 Mb) in all but one patient, and the deleted region common to all patients was delineated between two microsatellite markers (D8S1113 and D8S1763). This region was sequenced entirely from two overlapping bacterial artificial chromosomes. The common deleted region (120 kb) had a low GC content (37%), was composed more than 50% of LINE sequences, and contained only two candidate genes. The centromeric deletion borders were clustered within an interval of 33 kb between two microsatellite markers. This interval contains the first exon of an HMG-1-related gene (KIAA0808) and a putative gene, DL8q12, predicted to encode a protein with 231 amino acid residues with no homolog in protein databases. Analysis of the available mRNA from lymphoblastic cells of two patients with 8q12 deletions using common polymorphisms in the 3' UTR of KIAA0808 showed monoallelic expression of this gene. Identification of a biallelic polymorphism in the first exon of DL8q12 showed that this gene was deleted in two of four informative cases. Sequencing of the exons of both genes from all patients with 8q12 deletions did not show any mutation, which suggests that neither of these genes behaves as a classic tumor suppressor gene.

Published
2002

14. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

Author

Christian P. Vivarès, Gérard Prensier, Simone Duprat, Manolo Gouy, Emmanuel Cornillot, Valérie Barbe, Hicham El Alaoui, Michael Katinka, Patrick Wincker, William Saurin, Pierre Peyret, Philippe Brottier, Jean Weissenbach, Eric Peyretaillade, Frédéric Delbac, Guy Méténier, Fabienne Thomarat, 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), Laboratoire de Biologie des Protistes [Aubière] (LBP), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), 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)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and 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)

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Molecular Sequence Data, Protozoan Proteins, Mitosome, Genome, Mice, 03 medical and health sciences, parasitic diseases, Animals, Gene, Encephalitozoon cuniculi, 030304 developmental biology, Genomic organization, Genetics, 0303 health sciences, Multidisciplinary, biology, 030306 microbiology, fungi, Biological Transport, Sequence Analysis, DNA, DNA, Protozoan, biology.organism_classification, Biological Evolution, Mitochondria, Microsporidia, Polar tube, Eukaryote, Genome, Protozoan
Abstract

Microsporidia are obligate intracellular parasites infesting many animal groups. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage that diverged before the endosymbiotic event that led to mitochondria. The discovery of a gene for a mitochondrial-type chaperone combined with molecular phylogenetic data later implied that microsporidia are atypical fungi that lost mitochondria during evolution. Here we report the DNA sequences of the 11 chromosomes of the approximately 2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes). Genome compaction is reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The strong host dependence is illustrated by the lack of genes for some biosynthetic pathways and for the tricarboxylic acid cycle. Phylogenetic analysis lends substantial credit to the fungal affiliation of microsporidia. Because the E. cuniculi genome contains genes related to some mitochondrial functions (for example, Fe-S cluster assembly), we hypothesize that microsporidia have retained a mitochondrion-derived organelle.

Published
2001
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results