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1. Evidence for the dispersal of a unique lineage from Asia to America and Africa in the sugarcane fungal pathogen Ustilago scitaminea

Author

Athiappan Selvi, Caroline Calatayud, Karine Miranda Oliveira, Rosalyn Luzaran, Angélique D'Hont, Philippe Brottier, Florence Paulet, Olivier Garsmeur, Louis-Marie Raboin, Marie-Françoise Zapater, and Jean Carlier

Subjects
Asia, Lineage (genetic), Zoology, Outcrossing, Descendance, Microbiology, Autofécondation forcée, Variation génétique, Génétique des populations, Lignée, Botany, Ustilago, Genetics, Structure de la population, Outbreeding, Phylogeny, H20 - Maladies des plantes, Ustilago scitaminea, Genetic diversity, Saccharum officinarum, biology, Sugarcane smut, Microsatellite, Genetic Variation, Selfing, Spores, Fungal, biology.organism_classification, Saccharum, Genetics, Population, Africa, Smut, Biological dispersal, Americas, Microsatellite Repeats, Founder effect
Abstract

The basidiomycete Ustilago scitaminea Sydow, which causes sugarcane smut disease, has been spreading throughout Africa and America since the 1940s. The genetic diversity and structure of different populations of this fungus worldwide was investigated using microsatellites. A total of 142 single-teliospore were isolated from 77 distinct whips (sori) collected in 15 countries worldwide. Mycelium culture derived from on generation of selfing of these single teliospores were analysed for their polymorphisms at 17 microsatellite loci. All these strains but one were homozygous at all loci, indicating that selfing is likely the predominant reproductive mode of U. scitaminea. The genetic diversity of either American or African U. scitaminea populations was found to be extremely low and all strains belong to a single lineage. This lineage was also found in some populations of Asia, where most U. scitaminea genetic diversity was detected, suggesting that this fungal species originated from this region. The strong founder effect observed in U. scitaminea African and American populations suggests that the fungus migrated from Asia to other continents on rare occasions through movement of infected plant material. © 2006 Elsevier Inc. All rights reserved.

Published
2007
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2. Microsatellite markers in Carica papaya L.: isolation, characterization and transferability to Vasconcellea species

Author

Yann Froelicher, Ange-Marie Risterucci, Patrick Ollitrault, John Albeiro Ocampo Perez, Géo Coppens D'Eeckenbrugge, Dominique Dambier, and Philippe Brottier

Subjects
Transferability, Banque de gènes, Polymorphisme, Biology, Biochemistry, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, Genus, Botany, Genotype, Marqueur génétique, Vasconcellea, Ecology, Carica papaya, Microsatellite, biology.organism_classification, Carica, Génotype
Abstract

A dinucleotide microsatellite-enriched genomic library was obtained from Carica papaya L. Sixty-nine microsatellites were evaluated on three genotypes of C. papaya and seven species of the neighbour genus Vasconcellea. Among them, 45 markers were characterized on a sample of 29 accessions of C. papaya from the Caribbean region and 11 accessions of Vasconcellea from the Andes of Colombia and Ecuador. Twenty-four gave polymorphism in C. papaya and only four among the seven species of Vasconcellea, confirming the divergence between both genera. (Resume d'auteur)

Published
2006
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3. Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.)

Author

Rajinder Singh, Enrique Ritter, Philippe Amblard, D. Asmono, Ange-Marie Risterucci, Suan-Choo Cheah, Norbert Billotte, Tristan Durand-Gasselin, Benjamin Adon, H. Asmady, André Charrier, Philippe Brottier, Brigitte Courtois, Claire Billot, Nicolas Marseillac, Ana Herran, Wolfgang Rohde, Franc-Christophe Baurens, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de Recherche Agronomique de Côte d'Ivoire (CNRA), Bayer Cropscience, Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Malaysian Palm Oil Board, Centro de Arkaute, Partenaires INRAE, and SOCFINDO (P.T. Socfin Indonesia)

Subjects
0106 biological sciences, Genetic Linkage, Polymorphisme génétique, Arecaceae, Breeding, Elaeis guineensis, Polymerase Chain Reaction, 01 natural sciences, F30 - Génétique et amélioration des plantes, Marqueur génétique, Genetics, QUANTITATIVE TRAIT LOCI, 0303 health sciences, education.field_of_study, CONSTRUCTION, biology, Liaison génétique, Chromosome Mapping, food and beverages, General Medicine, PCR, AFLP MARKERS, Microsatellite, RFLP, Biotechnology, Population, Locus (genetics), Chromosomes, Plant, 03 medical and health sciences, Gene mapping, Botany, PLANTS, education, DNA Primers, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Polymorphism, Genetic, SEQUENCES, L, biology.organism_classification, Elaeis, Carte génétique, Amplified fragment length polymorphism, Huile de palme, Agronomy and Crop Science, Microsatellite Repeats, 010606 plant biology & botany
Abstract

International audience; A microsatellite-based high-density linkage map for oil palm (Elaeis guinensis Jacq.) was constructed from a cross between two heterozygous parents, a tenera palm from the La Me population (LM2T) and a dura palm from the Deli population (DA10D). A set of 390 simple sequence repeat (SSR) markers was developed in oil palm from microsatellite-enriched libraries and evaluated for polymorphism along with 21 coconut SSRs. A dense and genome-wide microsatellite framework as well as saturating amplified fragments length polymorphisms (AFLPs) allowed the construction of a linkage map consisting of 255 microsatellites, 688 AFLPs and the locus of the Sh gene, which controls the presence or absence of a shell in the oil palm fruit. An AFLP marker E-Agg/M-CAA132 was mapped at 4.7 cM from the Sh locus. The 944 genetic markers were distributed on 16 linkage groups (LGs) and covered 1,743 cM. Our linkage map is the first in oil palm to have 16 independent linkage groups corresponding to the plant's 16 homologous chromosome pairs. It is also the only high-density linkage map with as many microsatellite markers in an Arecaceae species and represents an important step towards quantitative trait loci analysis and physical mapping in the E. guineensis species.

Published
2005
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4. The DNA sequence and analysis of human chromosome 14

Author

Roland Heilig, Ralph Eckenberg, Jean-Louis Petit, Núria Fonknechten, Corinne Da Silva, Laurence Cattolico, Michaël Levy, Valérie Barbe, Véronique de Berardinis, Abel Ureta-Vidal, Eric Pelletier, Virginie Vico, Véronique Anthouard, Lee Rowen, Anup Madan, Shizhen Qin, Hui Sun, Hui Du, Kymberlie Pepin, François Artiguenave, Catherine Robert, Corinne Cruaud, Thomas Brüls, Olivier Jaillon, Lucie Friedlander, Gaelle Samson, Philippe Brottier, Susan Cure, Béatrice Ségurens, Franck Anière, Sylvie Samain, Hervé Crespeau, Nissa Abbasi, Nathalie Aiach, Didier Boscus, Rachel Dickhoff, Monica Dors, Ivan Dubois, Cynthia Friedman, Michel Gouyvenoux, Rose James, Anuradha Madan, Barbara Mairey–Estrada, Sophie Mangenot, Nathalie Martins, Manuela Ménard, Sophie Oztas, Amber Ratcliffe, Tristan Shaffer, Barbara Trask, Benoit Vacherie, Chadia Bellemere, Caroline Belser, Marielle Besnard-Gonnet, Delphine Bartol–Mavel, Magali Boutard, Stéphanie Briez-Silla, Stephane Combette, Virginie Dufossé-Laurent, Carolyne Ferron, Christophe Lechaplais, Claudine Louesse, Delphine Muselet, Ghislaine Magdelenat, Emilie Pateau, Emmanuelle Petit, Peggy Sirvain-Trukniewicz, Arnaud Trybou, Nathalie Vega-Czarny, Elodie Bataille, Elodie Bluet, Isabelle Bordelais, Maria Dubois, Corinne Dumont, Thomas Guérin, Sébastien Haffray, Rachid Hammadi, Jacqueline Muanga, Virginie Pellouin, Dominique Robert, Edith Wunderle, Gilbert Gauguet, Alice Roy, Laurent Sainte-Marthe, Jean Verdier, Claude Verdier-Discala, LaDeana Hillier, Lucinda Fulton, John McPherson, Fumihiko Matsuda, Richard Wilson, Claude Scarpelli, Gábor Gyapay, Patrick Wincker, William Saurin, Francis Quétier, Robert Waterston, Leroy Hood, and Jean Weissenbach

Subjects
Chromosomes, Human, Pair 14, Base Composition, Multidisciplinary, Molecular Sequence Data, Immunity, Reproducibility of Results, Genomics, Sequence Analysis, DNA, Physical Chromosome Mapping, DNA, Mitochondrial, DNA, Ribosomal, Synteny, Mice, Open Reading Frames, Genes, Animals, Humans, Chromosomes, Artificial, CpG Islands, 5' Untranslated Regions, Pseudogenes, Microsatellite Repeats
Abstract

Chromosome 14 is one of five acrocentric chromosomes in the human genome. These chromosomes are characterized by a heterochromatic short arm that contains essentially ribosomal RNA genes, and a euchromatic long arm in which most, if not all, of the protein-coding genes are located. The finished sequence of human chromosome 14 comprises 87,410,661 base pairs, representing 100% of its euchromatic portion, in a single continuous segment covering the entire long arm with no gaps. Two loci of crucial importance for the immune system, as well as more than 60 disease genes, have been localized so far on chromosome 14. We identified 1,050 genes and gene fragments, and 393 pseudogenes. On the basis of comparisons with other vertebrate genomes, we estimate that more than 96% of the chromosome 14 genes have been annotated. From an analysis of the CpG island occurrences, we estimate that 70% of these annotated genes are complete at their 5' end.

Published
2003
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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. Spastin, a new AAA protein, is altered in the most frequent form of autosomal dominant spastic paraplegia

Author

Jamilé Hazan, Alexis Brice, Jean Weissenbach, Nuria Fonknechten, François Artiguenave, Bertrand Fontaine, Delphine Mavel, Jean-Marc Burgunder, Roland Heilig, Jean-François Prud'homme, Corinne Cruaud, Valérie Barbe, Laurence Cattolico, Delphine Samson, Philippe Brottier, Patrick Wincker, Caroline Paternotte, Claire-Sophie Davoine, and Alexandra Durr

Subjects
Candidate gene, Spastin, Protein family, Positional cloning, Sequence analysis, Hereditary spastic paraplegia, Amino Acid Motifs, DNA Mutational Analysis, Molecular Sequence Data, Locus (genetics), Biology, Oxidative Phosphorylation, Mice, Genetics, medicine, Animals, Humans, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Cells, Cultured, Adenosine Triphosphatases, Expressed Sequence Tags, Base Sequence, Sequence Homology, Amino Acid, Paraplegin, Spastic Paraplegia, Hereditary, Exons, medicine.disease, Introns, Mitochondria, Muscle, Mutation, Sequence Alignment
Abstract

Autosomal dominant hereditary spastic paraplegia (AD-HSP) is a genetically heterogeneous neurodegenerative disorder characterized by progressive spasticity of the lower limbs. Among the four loci causing AD-HSP identified so far, the SPG4 locus at chromosome 2p2-1p22 has been shown to account for 40-50% of all AD-HSP families. Using a positional cloning strategy based on obtaining sequence of the entire SPG4 interval, we identified a candidate gene encoding a new member of the AAA protein family, which we named spastin. Sequence analysis of this gene in seven SPG4-linked pedigrees revealed several DNA modifications, including missense, nonsense and splice-site mutations. Both SPG4 and its mouse orthologue were shown to be expressed early and ubiquitously in fetal and adult tissues. The sequence homologies and putative subcellular localization of spastin suggest that this ATPase is involved in the assembly or function of nuclear protein complexes.

Published
1999
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8. Development of DNA microsatellite markers in tropical yam (Dioscorea sp.)

Author

Jean Louis Pham, Jean-Leu Marchand, Nora Scarcelli, Jean-Louis Noyer, Philippe Brottier, and Serge Tostain

Subjects
Dioscorea alata, Biochemistry, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, chemistry.chemical_compound, Igname, Botany, Marqueur génétique, Dioscorea abyssinica, Ecology, biology, Dioscorea, Microsatellite, biology.organism_classification, Sequence repeat, chemistry, Polymorphic locus, Dioscorea praehensilis, DNA
Abstract

We developed new simple sequence repeat (SSR) markers in different species of yam (Dioscorea sp.). A microsatellite-enriched bank was created from Dioscorea alata, Dioscorea abyssinica and Dioscorea praehensilis. Sixteen polymorphic loci were characterized. Several of these markers are transferable to species of other Dioscorea sections. (Resume d'auteur)

Published
2006
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9. A new set of microsatellite markers for the peach palm (Bactris gasipaes Kunth); characterization and across-taxa utility within the tribe Cocoeae

Author

Philippe Brottier, Thomas L. P. Couvreur, Bernard Perthuis, M. Vallejo, Jean-Christophe Pintaud, Jean-Louis Noyer, Norbert Billotte, Jean-Pierre Jacquemoud-Collet, Nicolas Marseillac, and Ange-Marie Risterucci

Subjects
Séquence nucléotidique, Bactris, Tribe (biology), Biochemistry, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, Gene flow, Bactris gasipaes, Domestication, Variation génétique, Peach palm, Botany, Across-taxa utility, Ressource génétique, Genetic diversity, Ecology, biology, Microsatellite, Elaeis, biology.organism_classification, Biosystematiek, Astrocaryum, Biosystematics
Abstract

A (GA)n microsatellite-enriched library was constructed and a new set of 18 nuclear simple sequence repeat loci was isolated in Bactris gasipaes var. gasipaes. The loci were found to be highly variable in the target species and readily transferable to related Bactris species as well as to the Astrocaryum and Elaeis genera of the same Cocoeae tribe. These microsatellite resources are made available to study the genetic diversity and gene flow within the Bactris complex for a better understanding of the domestication process of the peach palm and for further Cocoeae genetics.

Published
2004
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10. Nuclear microsatellite markers for the date palm (Phoenix dactylifera L.): characterization and utility across the genus Phoenix and in other palm genera

Author

Jean-Christophe Pintaud, Norbert Billotte, Marie-Hélène Chevallier, Jean-Louis Noyer, Thomas L. P. Couvreur, Nicolas Marseillac, Philippe Brottier, C. Moreau, Jean-Pierre Jacquemoud-Collet, and Ange-Marie Risterucci

Subjects
Germplasm, Séquence nucléotidique, Elaeis guineensis, Biochemistry, Phoenix, General Biochemistry, Genetics and Molecular Biology, diversity, F30 - Génétique et amélioration des plantes, Botany, Marqueur génétique, Genetic diversity, Ecology, biology, Microsatellite, biology.organism_classification, Biosystematiek, Phoenix dactylifera, Astrocaryum, PCR, Pritchardia, Biosystematics
Abstract

A (GA)n microsatellite-enriched library was constructed and 16 nuclear simple sequence repeat (SSR) loci were characterized in Phoenix dactylifera. Across-taxa amplification and genotyping tests showed the utility of most SSR markers in 11 other Phoenix species and the transferability of some of them in Elaeis guineensis, 11 species of Pritchardia, Pritchardiopsis jeanneneyi and six species of Astrocaryum. The first to be published for P. dactylifera, these new SSR resources are available for cultivar identification, pedigree analysis, germplasm diversity as well as genetic mapping studies.

Published
2004
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11. Characterization of microsatellite markers in mandarin orange (Citrus reticulata Blanco)

Author

Patrick Ollitrault, Gilles Costantino, Samia Lotfy, Yann Froelicher, Vincent Beaumont, Dominique Dambier, Jean Baptiste Bassene, Philippe Brottier, François Luro, Ange-Marie Risterucci, Christophe Didout, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Station de recherches agronomiques de San Giuliano, Institut National de la Recherche Agronomique (INRA), Institut national de la recherche agronomique [Maroc] (INRA Maroc), Centre de recherche Pernod Ricard, and Bayer Cropscience

Subjects
0106 biological sciences, Identification, Polymorphisme génétique, DIVERSITY, Orange (colour), 01 natural sciences, Mandarin Chinese, F30 - Génétique et amélioration des plantes, Loss of heterozygosity, Plante sauvage, chemistry.chemical_compound, Molecular marker, Hétérozygote, Genomic library, Marqueur génétique, GENETIQUE VEGETALE, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Genetics, 0303 health sciences, MOLECULAR MARKER, STMS, F70 - Taxonomie végétale et phytogéographie, GENOMIQUE, Horticulture, RUTACEAE, MANDARINIER, language, Microsatellite, Biotechnology, GENETIC, CARTOGRAPHIE GENETIQUE, Biology, 03 medical and health sciences, Variation génétique, CITRUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic diversity, biology.organism_classification, language.human_language, Rutaceae, chemistry, Collection de matériel génétique, Citrus reticulata, 010606 plant biology & botany
Abstract

International audience; A dinucleotide-enriched genomic library was obtained from mandarin orange (Citrus reticulata Blanco). A subset of 101 positive clones was sequenced and primers were designed. The loci were screened for levels of variation using 26-29 wild mandarin oranges collected in Vietnam. Forty-three loci were polymorphic with the number of alleles ranging from two to 18. The observed heterozygosity (H-O) and expected heterozygosity (H-E) were from 0.03 to 0.96 and from 0.03 to 0.92, respectively.

Published
2011
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12. 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
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13. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers

Author

Marc Giband, Philippe Brottier, Trung-Bieu Nguyen, Ange-Marie Risterucci, and Jean-Marc Lacape

Subjects
Identification, Population, Gossypium hirsutum, Biology, Gossypium, Genome, F30 - Génétique et amélioration des plantes, Polyploidy, chemistry.chemical_compound, Polymorphism (computer science), Molecular marker, Genetics, Genomic library, Marqueur génétique, education, DNA Primers, Gene Library, education.field_of_study, Polymorphism, Genetic, Génome, Chromosome Mapping, food and beverages, Microsatellite, Sequence Analysis, DNA, General Medicine, Gossypium barbadense, biology.organism_classification, chemistry, Hybridization, Genetic, Agronomy and Crop Science, Genome, Plant, Microsatellite Repeats, Biotechnology
Abstract

Microsatellite [simple-sequence repeat (SSR)] markers were developed and positioned on the genetic map of tetraploid cotton. Three hundred and ninety-two unique microsatellite sequences, all but two containing a (CA/GT) repeat, were isolated, and the deduced primers were used to screen for polymorphism between the Gossypium hirsutum and G. barbadense parents of the mapping population analyzed in our laboratory. The observed rate of polymorphism was 56%. The 204 polymorphic SSRs revealed 261 segregating bands, which ultimately gave rise to 233 mapped loci. The updated status of our genetic map is now of 1,160 loci and 5,519 cM, with an average distance between two loci of 4.8 cM. The presence of a total of 466 microsatellite loci, with an average distance of 12 cM between two SSR loci, now provides wide coverage of the genome of tetraploid cotton and thus represents a powerful means for the production of a consensus map and for the effective tracking of QTLs.

Published
2004

14. A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers

Author

Claire Lanaud, M. Abouladze, Brigitte Courtois, Jeanne A.K. N'Goran, Didier Clément, Ange-Marie Risterucci, Tatiana Pugh, C. Deletrez, Philippe Brottier, Olivier Fouet, and Pierre Larmande

Subjects
Population, Distribution des populations, Biology, Genome, F30 - Génétique et amélioration des plantes, Variation génétique, Gene mapping, Genetic linkage, Genetics, Theobroma cacao, Marqueur génétique, Genomic library, education, Crosses, Genetic, DNA Primers, Linkage (software), education.field_of_study, Cacao, Genomic Library, Génome, Polymorphism, Genetic, Microsatellite, Chromosome Mapping, General Medicine, Carte génétique, RFLP, Restriction fragment length polymorphism, Agronomy and Crop Science, Polymorphism, Restriction Fragment Length, Biotechnology, Microsatellite Repeats
Abstract

A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resis- tance and defence gene analogs (Rgenes-RFLP) previ- ously mapped in cacao. A genomic library enriched for (GA)n and (CA)n was constructed, and 201 new mi- crosatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Ama- zon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identi- fication and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.

Published
2003

15. 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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16. 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
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17. 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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18. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence

Author

Jean Weissenbach, Corinne Dasilva, William Saurin, Philippe Brottier, Patrick Wincker, Olivier Jaillon, Alain Bernot, H. Roest Crollius, F Quétier, Cécile Fischer, Laurence Bouneau, Cécile Fizames, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
Comparative genomics, Genetics, Genome evolution, biology, [SDV]Life Sciences [q-bio], Genome project, Computational biology, Tetraodon nigroviridis, biology.organism_classification, ENCODE, Genome, Gene density, Reference genome
Abstract

The number of genes in the human genome is unknown, with estimates ranging from 50,000 to 90,000 (refs 1, 2), and to more than 140,000 according to unpublished sources. We have developed 'Exofish', a procedure based on homology searches, to identify human genes quickly and reliably. This method relies on the sequence of another vertebrate, the pufferfish Tetraodon nigroviridis, to detect conserved sequences with a very low background. Similar to Fugu rubripes, a marine pufferfish proposed by Brenner et al. as a model for genomic studies, T. nigroviridis is a more practical alternative with a genome also eight times more compact than that of human. Many comparisons have been made between F. rubripes and human DNA that demonstrate the potential of comparative genomics using the pufferfish genome. Application of Exofish to the December version of the working draft sequence of the human genome and to Unigene showed that the human genome contains 28,000-34,000 genes, and that Unigene contains less than 40% of the protein-coding fraction of the human genome.

Published
2000
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19. Mutant WD-repeat protein in triple-A syndrome

Author

Laurence Cattolico, Clothilde Penet, Danielle Naville, Jean-Louis Chaussain, Marc Nicolino, B. Chaouachi, Arnold Munnich, Jean Weissenbach, Smail Hadj-Rabia, Martine Begeot, Claude Mugnier, Fawzi Bakiri, Stanislas Lyonnet, Anna Tullio-Pelet, Marc-Henri de Laet, Philippe Brottier, Rémi Salomon, Communications Cellulaires et Différenciation (CCD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
Chromosomes, Artificial, Bacterial, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Amino Acid Motifs, DNA Mutational Analysis, Alacrima, Linkage Disequilibrium, SYNDROME TRIPLE-A, Consanguinity, Africa, Northern, Expressed Sequence Tags, Genetics, EXPRESSION DU GENE, Syndrome, Pedigree, [SDV] Life Sciences [q-bio], medicine.symptom, Repetitive Sequences, Amino Acid, medicine.medical_specialty, Allgrove Syndrome, Molecular Sequence Data, Nerve Tissue Proteins, Biology, Triple-A syndrome, Evolution, Molecular, Species Specificity, Internal medicine, Xerophthalmia, medicine, Adrenal insufficiency, Humans, Point Mutation, Abnormalities, Multiple, Amino Acid Sequence, Codon, Chromosomes, Human, Pair 12, SURRENALE, Sequence Homology, Amino Acid, Cerebellar ataxia, Haplotype, Proteins, medicine.disease, Esophageal Achalasia, Nuclear Pore Complex Proteins, Endocrinology, Peripheral neuropathy, Genes, Haplotypes, Nervous System Diseases, Sequence Alignment, Adrenal Insufficiency
Abstract

Triple-A syndrome (MIM 231550; also known as Allgrove syndrome) is an autosomal recessive disorder characterized by adrenocorticotropin hormone (ACTH)-resistant adrenal insufficiency, achalasia of the oesophageal cardia and alacrima1,2,3. Whereas several lines of evidence indicate that triple-A syndrome results from the abnormal development of the autonomic nervous system4,5,6, late-onset progressive neurological symptoms (including cerebellar ataxia, peripheral neuropathy and mild dementia) suggest that the central nervous system may be involved in the disease as well7,8. Using fine-mapping based on linkage disequilibrium in North African inbred families, we identified a short ancestral haplotype on chromosome 12q13 (

Published
2000

20. Correction: Initial sequencing and analysis of the human genome

Author

Paul Predki, John Sulston, William Morris, Sarah Wenning, Jun Gu, Danielle Thierry-Mieg, Roger A. Schultz, Michael J. Morgan, Michael Doyle, Joseph Szustakowki, Lorenzo Cerutti, A. Coulson, Alex Bateman, Patrick Wincker, Michael C. Zody, Mark T. Ross, Paul G. Richardson, Keri Devon, Yasushi Totoki, Karsten Hokamp, George M. Weinstock, John Howland, Arek Kaspryzk, James G. R. Gilbert, Cher Miranda, Aristides Patrinos, William Saurin, A. Pia Abola, Kazuhiko Kawasaki, John Bouck, Marvin Frazier, Wonhee Jang, Jan Fang Cheng, Stephanie L. Chissoe, Matthew C. Jones, Glen A. Evans, Huanming Yang, Daniel G. Brown, Richard Durbin, Jennifer Baldwin, Tracie L. Miner, Asif T. Chinwalla, Arian F.A. Smit, C M Clee, Elaine R. Mardis, Henning Hermjakob, Nicole Stange-Thomann, Maynard V. Olson, Jian Wang, Cyrus L. Harmon, Shiaw Pyng Yang, André Rosenthal, Catherine Robert, Masahira Hattori, Jane Peterson, Ratna Shownkeen, Maria Athanasiou, Christopher B. Burge, Erica Sodergren, Carrie Sougnez, Lynn Doucette-Stamm, Hidemi Watanabe, Ronald W. Davis, Tarjei S. Mikkelsen, Mark Rosetti, Christopher J. Elkin, Todd M. Lowe, LaDeana W. Hillier, Jane Grimwood, Kazutoyo Osoegawa, Richard R. Copley, Simon Kasif, Joseph J. Catanese, Keith Weinstock, Lee Rowen, Roel Funke, Paul Kitts, Lukas Wagner, Guy Slater, Anne S. Olsen, Edward Uberbacher, Lucinda Fulton, Andrew Dunham, Andrew Heaford, David Kulp, Elbert Branscomb, William Fitzhugh, Eugene V. Koonin, Leroy Hood, Anup Madan, Jean Thierry-Mieg, Richard Reinhardt, Kim C. Worley, Richard M. Myers, Dudley Wyman, Jean Weissenbach, David R. Bentley, Panos Deloukas, Philippe Brottier, H. Blöcker, Stephan Beck, Marc Rubenfield, Terrence S. Furey, Ken Dewar, Michael L. Metzker, Rajinder Kaul, Guyang Huang, Hsiu Chuan Chen, Ewan Birney, Warren Gish, John Douglas Mcpherson, Asao Fujiyama, Aoife McLysaght, Shinsei Minoshima, Sandra W. Clifton, Lisa Kann, R Ainscough, K. Hornischer, Simon G. Gregory, Lauren Linton, Kim D. Delehaunty, James C. Mullikin, Neilay Dedhia, Matthias Platzer, Gerald Nyakatura, John V. Moran, Andrew J. Mungall, Chiharu Kawagoe, François Artiguenave, Deanna M. Church, Elia Stupka, Jun Yu, Peer Bork, Evan E. Eichler, L. Aravind, James H. Gorrell, Bruce A. Roe, Raymond Wheeler, Norman A. Doggett, Douglas R. Smith, Yu Juin Chen, David Haussler, Todd D. Taylor, Stefan Taudien, Susan Lucas, Rebecca Deadman, Hans Lehrach, Hiroaki Shizuya, Doron Lancet, Greg Schuler, Nigel P. Carter, John Burton, Huaqin Pan, Eric S. Lander, Andreas Rump, Nikola Stojanovic, Victor J. Pollara, Alan Williams, Melissa De La Bastide, W. James Kent, Mark S. Guyer, Nicola Mulder, Sarah Milne, Bruce W. Birren, John W. Wallis, Joann Dubois, Tom Slezak, Lisa Cook, Raju Kucherlapati, Andrew Delehaunty, Lucy Matthews, Ian Dunham, L. Steven Johnson, Robert H. Waterston, Andrew Sheridan, Jörg Schultz, Nancy A. Federspiel, Jason B. Kramer, Tim Hubbard, Ru Fang Yeh, Steven E. Scherer, Francis S. Collins, David L. Nelson, Sean Humphray, Tobias Doerks, Chad Nusbaum, Darren Grafham, Mei Lee Hong, Michael Proctor, Christopher K. Raymond, Diane Gage, Kris A. Wetterstrand, Feng Chen, Simon Mercer, Thomas A. Jones, Trevor Hawkins, Aravind Subramanian, Jeffrey A. Bailey, Amanda McMurray, Serafim Batzoglou, Jeremy Schmutz, Jill P. Mesirov, Shizen Qin, Rosie Levine, Adam Felsenfeld, Thomas Brüls, Kevin McKernan, Michele E. Clamp, Christine Lloyd, Susan L. Naylor, Gabriele Nordsiek, Jessica A. Lehoczky, Adrienne Hunt, Marco A. Marra, David R. Cox, Mark Dickson, Michael C. Wendl, Yuri I. Wolf, Jane Rogers, Ian F Korf, Eric Pelletier, Takehiko Itoh, Juliane Ramser, Robert S. Fulton, Sarah Sims, Richard A. Gibbs, Lisa French, Katrina Harris, Richa Agarwala, Christina Raymond, James Meldrim, Sangdun Choi, Richard K. Wilson, Patrick Minx, Douglas L. Johnson, Yoshiyuki Sakaki, Scot Kennedy, Pieter J. de Jong, Yoshihide Hayashizaki, W. Richard McCombie, Sean R. Eddy, Donna M. Muzny, Jerome Naylor, Paul A. McEwan, Atsushi Toyoda, Tetsushi Yada, Nobuyoshi Shimizu, Robert W. Plumb, Catherine M. Rives, Chris P. Ponting, Ralph Santos, Kenneth H. Wolfe, Kymberlie H. Pepin, Roland Heilig, and James E. Galagan

Subjects
Multidisciplinary, Correction, Human genome, Computational biology, Biology
Published
2001
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21. 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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22. 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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23. The Epitopic Dissection of the CD2 Defined Molecule: Relationship of the Second Workshop Antibodies in Terms of Reactivities with Leukocytes, Rosette Blocking Properties, Induction of Positive Modulation of the Molecule, and Triggering T Cell Activation

Author

Virginia Lepage, Philippe Brottier, Alain Bernard, Laurence Boumsell, and Eric Georget

Subjects
biology, Cluster of differentiation, Chemistry, medicine.drug_class, Stereochemistry, T cell, Monoclonal antibody, Molecular biology, Epitope, Sialic acid, chemistry.chemical_compound, medicine.anatomical_structure, Antigen, medicine, biology.protein, Antibody, Neuraminidase
Abstract

Before the era of monoclonal antibodies (mAbs), several reports indicated that the T cell surface molecule responsible for rosette formation with sheep erythrocytes (E) is a 50-Kd molecule (1,2). This was confirmed and extended by obtention of mAbs directed against this molecule (3–5) and the First International Workshop on Human Leucocyte Differentiation Antigens could define the typical clusters of differentiation as CD2 [T, gp50] with mAbs 9.6, 35.1, and T111 (6). We have also described another mAb, termed D66, reactive with the same molecule, but to a distinct epitope, since we observed no cross-blocking between the binding of D66 and the binding of 9.6/T111 antibodies. Several of our observations indicated that remarkable features characterize this epitope (4): the density of D66 is high on immature and activated T cells, whereas T-PBLs display only a low density of D66 epitopes; the low density of D66 on T-PBL can be explained, to a large extent, by their coverage with sialic acid residues (as such, D66 could not be classified, strictly speaking, as a CD2 mAb since the definition of CD by the First Workshop relied both on tissue distribution and M.W. determinations). In addition, D66 would not block T cell rosettes with E pretreated with AET or neuraminidase while it would efficiently block rosettes with untreated E, either at 4 or at 37°C. Moreover we observed a cell metabolism-independent positive modulation phenomenon of the CD2 defined molecule through the D66 epitope: binding of a second Ab, even an Fab fragment, on D66 mAb can totally reverse inhibition of E-rosette formation, and evidence that this is due to emergence of initially hidden D66 epitopes was provided by cytofluorometric studies.

Published
1986
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