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1. Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study

Author: Philippe Marullo, Pascal Durrens, Emilien Peltier, Margaux Bernard, Chantal Mansour, and Denis Dubourdieu
Subjects: QTL, OYE2, VHS1, Subtelomeric region, Wine yeast, Temperature, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Fermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. Among them, high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes. Results In this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genes VHS1 and OYE2 characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (> 240 g/L of sugar) carried out at high temperatures (> 28 °C). Phenotypes impacted were mostly related to the late stage of alcoholic fermentation during the stationary growth phase of yeast. Conclusions Our findings illustrate the complex genetic determinism of stuck fermentation and open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.
Published: 2019
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2. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

Author: Adrien Zimmer, Cécile Durand, Nicolás Loira, Pascal Durrens, David James Sherman, and Philippe Marullo
Subjects: Medicine, Science
Abstract: Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI) involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.
Published: 2014
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3. Fusion and fission of genes define a metric between fungal genomes.

Author: Pascal Durrens, Macha Nikolski, and David Sherman
Subjects: Biology (General), QH301-705.5
Abstract: Gene fusion and fission events are key mechanisms in the evolution of gene architecture, whose effects are visible in protein architecture when they occur in coding sequences. Until now, the detection of fusion and fission events has been performed at the level of protein sequences with a post facto removal of supernumerary links due to paralogy, and often did not include looking for events defined only in single genomes. We propose a method for the detection of these events, defined on groups of paralogs to compensate for the gene redundancy of eukaryotic genomes, and apply it to the proteomes of 12 fungal species. We collected an inventory of 1,680 elementary fusion and fission events. In half the cases, both composite and element genes are found in the same species. Per-species counts of events correlate with the species genome size, suggesting a random mechanism of occurrence. Some biological functions of the genes involved in fusion and fission events are slightly over- or under-represented. As already noted in previous studies, the genes involved in an event tend to belong to the same functional category. We inferred the position of each event in the evolution tree of the 12 fungal species. The event localization counts for all the segments of the tree provide a metric that depicts the "recombinational" phylogeny among fungi. A possible interpretation of this metric as distance in adaptation space is proposed.
Published: 2008
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4. The family based variability in protein family expansion.

Author: Anasua Sarkar, Macha Nikolski, and Pascal Durrens
Published: 2013
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5. Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.

Author: David James Sherman, Tiphaine C. Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, and Pascal Durrens
Published: 2009
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6. Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.

Author: David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, and Jean-Luc Souciet
Published: 2006
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7. Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.

Author: David James Sherman, Pascal Durrens, Emmanuelle Beyne, and Macha Nikolski
Published: 2004
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8. Many interspecific chromosomal introgressions are highly prevalent in HolarcticSaccharomyces uvarumstrains found in human-related fermentations

Author: Maria Chernova, Erwan Guichoux, Warren Albertin, David James Sherman, Isabelle Masneuf-Pomarède, Philippe Marullo, and Pascal Durrens
Subjects: 0301 basic medicine, Genetics, education.field_of_study, biology, 030106 microbiology, Saccharomyces eubayanus, Population, Introgression, Bioengineering, Locus (genetics), biology.organism_classification, Applied Microbiology and Biotechnology, Biochemistry, Saccharomyces, Genome, DNA sequencing, 03 medical and health sciences, 030104 developmental biology, Microsatellite, education, Biotechnology
Abstract: In the last two decades, the massive genome sequencing of strains belonging to the Saccharomyces genus revealed the complex reticulated evolution of this group. Among the various evolutionary mechanisms described, the introgression of large chromosomal regions resulting from interspecific hybridization has recently shed light on the Saccharomyces uvarum species. In this work we provide the de novo assembled genomes of four S. uvarum strains presenting more than 712 kb of introgressed loci inherited from both S. eubayanus and S. kudriavzevii species. In order to study the prevalence of such introgressions in a large population, we designed multiplexed PCR- markers able to survey the inheritance of 8 chromosomal regions. Our data confirm that introgressions are widely disseminated in Holarctic S. uvarum population and are more frequently found in strains isolated from human-related fermentations. According to the origin of the strains (nature, cider or wine related process) some loci are overrepresented suggesting their positive selection by human activity. Except one locus located on chromosome 7, the introgressions present a low level of heterozygozity similar to that observed for nine neutral markers (microsatellites). Finally, most of these loci tested showed an expected Mendelian segregation after meiosis and can recombined with their chromosomal counterpart in S. uvarum.
Published: 2017
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9. Natural allelic variations ofSaccharomyces cerevisiaeimpact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study

Author: Margaux Bernard, Chantal Mansour, Pascal Durrens, Philippe Marullo, Emilien Peltier, and Denis Dubourdieu
Subjects: education.field_of_study, Population, Saccharomyces cerevisiae, food and beverages, Ethanol fermentation, Biology, Quantitative trait locus, biology.organism_classification, Yeast, Stuck fermentation, Fermentation, Food science, education, Winemaking
Abstract: BackgroundFermentation completion is a major prerequisite in many industrial processes involving the bakery yeastSaccharomyces cerevisiae.Stuck fermentations can be due to the combination of many environmental stresses. Among them high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes.ResultsIn this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genesVHS1andOYE2characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (>240 g/L of sugar) carried out at high temperatures (>28°C). Phenotypes impacted were related to the late stage of alcoholic fermentation during the stationary growth phase of yeast.ConclusionsThe genes identified are related to molecular functions such as Programed Cell Death, ROS metabolism and respire-fermentative switch and were never related to fermentation efficiency. Our findings open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.
Published: 2019
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10. Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936

Author: Christophe Klopp, Isabelle Accoceberry, Nicolas Biteau, Pascal Durrens, Karine Dementhon, Valérie Fitton-Ouhabi, Thierry Noël, David James Sherman, 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, Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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 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, Plateforme Bio-Informatique - Génotoul, Institut National de la Recherche Agronomique (INRA), Plafrim, CPU, Genotoul Bioinfo, Laboratoire de Microbiologie Fondamentale et Pathogénicité UMR-CNRS 5234, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), ANR-10-EQPX-16-01, Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Fondamentale et Pathogénicité (MFP), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest
Subjects: 0301 basic medicine, Strain atcc, Whole genome sequencing, Genetics, congenital, hereditary, and neonatal diseases and abnormalities, Eukaryotes, Strain (biology), 030106 microbiology, Biology, Yeast, Microbiology, 03 medical and health sciences, 030104 developmental biology, Type (biology), Clavispora lusitaniae, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Chromosomal Structure, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Clade, Molecular Biology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology
Abstract: Clavispora lusitaniae , an environmental saprophytic yeast belonging to the CTG clade of Candida , can behave occasionally as an opportunistic pathogen in humans. We report here the genome sequence of the type strain CBS 6936. Comparison with sequences of strain ATCC 42720 indicates conservation of chromosomal structure but significant nucleotide divergence.
Published: 2017
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11. Molecular typing of wine yeast strains Saccharomyces bayanus var. uvarum using microsatellite markers

Author: Pascal Durrens, Marc Lollier, Isabelle Masneuf-Pomarède, C. Le Jeune, Michel Aigle, and Denis Dubourdieu
Subjects: Electrophoresis, Saccharomyces cerevisiae, Saccharomyces bayanus, Wine, Locus (genetics), Applied Microbiology and Biotechnology, Microbiology, Saccharomyces, 03 medical and health sciences, Typing, Mycological Typing Techniques, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Winemaking, Genetics, 0303 health sciences, biology, Chimera, 030306 microbiology, biology.organism_classification, Yeast in winemaking, Karyotyping, Microsatellite, Genome, Fungal, Microsatellite Repeats
Abstract: The Saccharomyces bayanus var. uvarum yeasts are associated with spontaneous fermentation of must. Some strains were shown to be enological yeasts of interest in different winemaking processes. The molecular typing of S. bayanus var. uvarum at the strain level has become significant for wine microbiologists. Four microsatellite loci were defined from the exploration of genomic DNA sequence of S. bayanus var. uvarum. The 40 strains studied were homozygote for the locus considered. The discriminating capacity of the microsatellite method was found to be equal to that of karyotypes analysis. Links between 37 indigenous strains with the same geographic origin could be established through the analysis of microsatellite patterns. The analysis of microsatellite polymorphism is a reliable method for wine S. bayanus var. uvarum strains and their hybrids with Saccharomyces cerevisiae identification in taxonomic, ecological studies and winemaking applications.
Published: 2007
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12. A systematic nomenclature of chromosomal elements for hemiascomycete yeasts

Author: Pascal Durrens, David James Sherman, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)
Subjects: 0106 biological sciences, Cancer genome sequencing, Bioengineering, comparative genomics, Computational biology, Biology, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, Genome, DNA sequencing, 03 medical and health sciences, Ascomycota, Terminology as Topic, Genetics, DNA, Fungal, Nomenclature, 030304 developmental biology, Comparative genomics, 0303 health sciences, Fungal genetics, Génolevures, Sequence Analysis, DNA, genome sequencing, genomic DNA, nomenclature, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Chromosomes, Fungal, Genome, Fungal, 010606 plant biology & botany, Biotechnology, Personal genomics
Abstract: International audience; We present a compact, stable, unambiguous and extensible nomenclature for unique chromosomal elements from genomic DNA, developed to meet the increasing need created by the increasing number of yeast sequencing projects. Our proposal, adopted for use in the Génolevures project, is specifically designed to facilitate basic tasks in comparative genomics.
Published: 2005
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13. Saccharomyces forkhead protein Fkh1 regulates donor preference during mating-type switching through the recombination enhancer

Author: Eric Coïc, Pascal Durrens, Zhiqi Zhou, James E. Haber, and Kaiming Sun
Subjects: Saccharomyces cerevisiae Proteins, Genes, Fungal, Molecular Sequence Data, Saccharomyces cerevisiae, Cell Cycle Proteins, Locus (genetics), Saccharomyces, Open Reading Frames, Forkhead Transcription Factors, Species Specificity, Sequence Homology, Nucleic Acid, Two-Hybrid System Techniques, Genetics, Gene conversion, Enhancer, Alleles, Recombination, Genetic, Binding Sites, Base Sequence, Models, Genetic, biology, fungi, DNA, Genes, Mating Type, Fungal, biology.organism_classification, Precipitin Tests, Chromatin, Open reading frame, Mating of yeast, Mutation, Gene Deletion, Research Paper, Transcription Factors, Developmental Biology
Abstract: Saccharomyces mating-type switching results from replacement by gene conversion of the MAT locus with sequences copied from one of two unexpressed donor loci, HML or HMR. MATa cells recombine with HMLα ∼90% of the time, whereas MATα cells choose HMRa 80%–90% of the time. HML preference in MATa is controlled by the cis-acting recombination enhancer (RE) that regulates recombination along the entire left arm of chromosome III. Comparison of RE sequences between S. cerevisiae, S. carlsbergensis, and S. bayanus defines four highly conserved regions (A, B, C, and D) within a 270-bp minimum RE. An adjacent E region enhances RE activity. Multimers of region A, D, or E are sufficient to promote selective use of HML. Regions A, D, and E each bind in vivo the transcription activator forkhead proteins Fkh1p and Fkh2p and their associated Ndd1p, although there are no adjacent open reading frames (ORFs). Deletion of FKH1significantly reduces MATa's use of HML, as does mutation of the Fkh1/Fkh2-binding sites in a multimer of region A. We conclude that Fkh1p regulates MATa donor preference through direct interaction with RE.
Published: 2002
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14. Diversity and variability of NOD-like receptors in fungi

Author: Marina Lamacchia, Bostjan Kobe, Sven J. Saupe, Matthieu Paoletti, David James Sherman, Pascal Durrens, Asen Daskalov, Witold Dyrka, Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institute for Molecular Bioscience and Centre for Infectious Disease Research, University of Queensland, plafrim, ANR-11-BSV3-0019,Mykimun,Reconnaissance hétérospécifique chez les champignons filamenteux : Des récepteurs à la réponse cellulaire(2011), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-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: NACHT, Reassortment, Molecular Sequence Data, Receptors, Cell Surface, Biology, Genome, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, NLR, Evolution, Molecular, Fungal Proteins, Genetics, Gene family, Amino Acid Sequence, Receptor, Gene, Ecology, Evolution, Behavior and Systematics, Research Articles, Conserved Sequence, Phylogeny, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Innate immune system, Concerted evolution, Polymorphism, Genetic, Effector, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Fungi, immunity, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Protein Structure, Tertiary, Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are intracellular receptors that control innate immunity and other biotic interactions in animals and plants. NLRs have been characterized in plant and animal lineages, but in fungi, this gene family has not been systematically described. There is however previous indications of the involvement of NLR-like genes in nonself recognition and programmed cell death in fungi. We have analyzed 198 fungal genomes for the presence of NLRs and have annotated a total of 5,616 NLR candidates. We describe their phylogenetic distribution, domain organization, and evolution. Fungal NLRs are characterized by a great diversity of domain organizations, suggesting frequently occurring combinatorial assortments of different effector, NOD and repeat domains. The repeat domains are of the WD, ANK, and TPR type; no LRR motifs were found. As previously documented for WD-repeat domains of fungal NLRs, TPR, and ANK repeats evolve under positive selection and show highly conserved repeats and repeat length polymorphism, suggesting the possibility of concerted evolution of these repeats. We identify novel effector domains not previously found associated with NLRs, whereas others are related to effector domains of plant or animals NLRs. In particular, we show that the HET domain found in fungal NLRs may be related to Toll/interleukin-1 receptor domains found in animal and plant immune receptors. This description of fungal NLR repertoires reveals both similarities and differences with plant and animals NLR collections, highlights the importance of domain reassortment and repeat evolution and provides a novel entry point to explore the evolution of NLRs in eukaryotes.
Published: 2014
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15. Deciphering the language of fungal pathogen recognition receptors

Author: Witold Dyrka, Pascal Durrens, Mathieu Paoletti, Sven Saupe, David James Sherman, Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), ANR-11-BSV3-0019,Mykimun,Reconnaissance hétérospécifique chez les champignons filamenteux : Des récepteurs à la réponse cellulaire(2011), 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, Wroclaw University of Technology [Wroclaw], from patterns to models in computational biodiversity and biotechnology (PLEIADE), 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 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-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Partially funded by ANR-11-BSV3-0019, Mykimun, Wroclaw University of Science and Technology, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Polish Bioinformatics Society, Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Dyrka, Witold, and BLANC - Reconnaissance hétérospécifique chez les champignons filamenteux : Des récepteurs à la réponse cellulaire - - Mykimun2011 - ANR-11-BSV3-0019 - BLANC - VALID
Subjects: fungi, amino acid repeats, innate immune system, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], unequal crossing-over, formal languages, string rewrit-ing system, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience; The immune system searches for pathogen invasion markers, which include pathogen proteins and host proteins modified in the course of the invasion. While some pathogen-associated molecular patterns are relatively invariant, numerous pathogen-specific markers change quickly. Therefore, to win the arms race with pathogens, host recognition receptors must adapt quickly to varied and modulating markers. To achieve this goal, the recognition domain of the receptor requires the capacity to recognize diverse possible pathogen molecule epitopes, and ability to quickly learn new ones. In plants and fungi, which lack an adaptive immune system, this key role in the immunity is played by the NLR family of receptors, which adapt to ever-changing pathogen-specific invasion markers thanks to their repeat-based architecture, which can produce diversity of recognition paratopes through unequal crossing-over and mutation [1]. The unequal crossing-over is a repeat shuffling process 10,000 to 100,000 times quicker than the standard point mutation, however it requires (and promotes) high sequence similarity between consecutive repeat units. At the same time certain positions in the repeats are highly variable under positive diversifying selection; they are believed to form the actual recognition paratope [2, 3]. Characterizing computationally the language of these pathogen recognition receptors can provide insight into the molecular mechanisms of immune response and describe the limits of the pathogen targets that can be recognized.In this work, we modeled generation and selection of the recognition paratopes as a stochastic string rewriting system with constraints, tuned by analysis of observed evolutionary processes and validated with regard to a large data set of fungal NLR [3]. First, we cross-checked the unequal crossing-over and mutation model with the existing experimental data. Second, we analyzed mathematical properties of the model and showed that its convergence to stationary distribution. Then, we compared real and simulated data. Among others, analyzing the feasibleset of solutions revealed that the model explained the i=i+2 (even-odd) periodicity observed in the repeat number distribution of a family of receptors. Next, we explored discrepancies between real and simulated data in order to discover constraints acting on the paratopes. For example, by comparing amino acid content in the model and original populations, we confirmed that highly variable sites identified on the basis of entropy, were subject to constraints towards composition typical for binding sites, which was coherent with the suggested role of recognition paratopes. Finally, we proposed an interactive approach to exploring the solution space of amino acid repeats by means of 2-d projections and significance tests in sectors of the space. In a preliminary analysis, we found an overrepresented pattern R-[SYQFW](1,3)-R at one of the highly variable positions in a family of receptors, which potentially has functional importance.The methodology developed in this work is general and therefore can be applied to any class of amino acid repeats generated by unequal crossing-over for which an equivalent high quality data set is available. An appealing future application of our model would be testing ofhypotheses regarding repeat origin or function encoded as constraints on the string rewriting system. [1] M.Paoletti, S.J.Saupe. BioEssays, 2009, 31:1201-1210[2] M.Paoletti, S.J.Saupe, C.Clave, PLoS ONE, 2007, 2:e283[3] W.Dyrka, M.Lamacchia, P.Durrens, B.Kobe, A.Daskalov, M.Paoletti, D.J.Sherman, S.Saupe, Gen Biol Evol, 2014, 6, 3137-3158.
Published: 2014

16. Draft genome sequence of Rhodosporidium toruloides CECT1137, an oleaginous yeast of biotechnological interest

Author: David James Sherman, Pascal Durrens, Xavier Calcas, Nicolas Morin, Cécile Neuvéglise, Hugo Devillers, Jean-Marc Nicaud, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)
Subjects: Whole genome sequencing, Eukaryotes, [SDV]Life Sciences [q-bio], Rhodosporidium toruloides, Computational biology, Genome project, Biology, biology.organism_classification, C content, Yeast, Microbiology, séquençage du génome, Genetics, basidiomycète, levure, Molecular Biology, Gene
Abstract: We report the sequencing of the basidiomycetous yeast Rhodosporidium toruloides CECT1137. The current assembly comprises 62 scaffolds, for a total size of ca. 20.45 Mbp and a G+C content of ca. 61.9%. The genome annotation predicts 8,206 putative protein-coding genes.
Published: 2014
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17. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum

Author: José Paulo Sampaio, David James Sherman, Paula Gonçalves, Pedro Almeida, Isabelle Masneuf-Pomarède, Diego Libkind, Philippe Marullo, Carla Gonçalves, Warren Albertin, Sara Teixeira, Chris Todd Hittinger, Martin Bontrager, Pascal Durrens, Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, CICECO, Universidade de Aveiro, IFREMER- Département Etude des Ecosystèmes Profonds (DEEP/LEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Instituto Nacional de Investigaciones en Biodiversidad y Medioambiente [Bariloche] (INIBIOMA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), University of Wisconsin-Madison, Faculté d'Oenologie [Bordeaux II], Université Bordeaux Segalen - Bordeaux 2-Institut des Sciences de la Vigne et du Vin (ISVV), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), 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, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Aquitaine Region grants 20030304002FA, 20040305003FA and SAGESSE, Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Evolution, Population, General Physics and Astronomy, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Article, General Biochemistry, Genetics and Molecular Biology, purl.org/becyt/ford/1 [https], Domestication, Ciencias Biológicas, Population genomics, Saccharomyces, Biología Celular, Microbiología, Botany, Patagonia, Genetics, purl.org/becyt/ford/1.6 [https], DNA, Fungal, education, 2. Zero hunger, Wine, Fermentation in winemaking, Genetic diversity, education.field_of_study, Multidisciplinary, Saccharomyces eubayanus, Fungal genetics, Genetic Variation, food and beverages, Genomics, General Chemistry, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Phylogeography, Evolutionary biology, Fermentation, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], CIENCIAS NATURALES Y EXACTAS
Abstract: In addition to Saccharomyces cerevisiae, the cryotolerant yeast species S. uvarum is also used for wine and cider fermentation but nothing is known about its natural history. Here we use a population genomics approach to investigate its global phylogeography and domestication fingerprints using a collection of isolates obtained from fermented beverages and from natural environments on five continents. South American isolates contain more genetic diversity than that found in the Northern Hemisphere. Moreover, coalescence analyses suggest that a Patagonian sub-population gave rise to the Holarctic population through a recent bottleneck. Holarctic strains display multiple introgressions from other Saccharomyces species, those from S. eubayanus being prevalent in European strains associated with humandriven fermentations. These introgressions are absent in the large majority of wild strains and gene ontology analyses indicate that several gene categories relevant for wine fermentation are overrepresented. Such findings constitute a first indication of domestication in S. uvarum. Fil: Almeida, Pedro. Universidade Nova de Lisboa; Portugal Fil: Goncalves, Carla. Universidade Nova de Lisboa; Portugal Fil: Teixeira, Sara. Universidade Nova de Lisboa; Portugal Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina. Universidad Nacional del Comahue; Argentina Fil: Bontrager, Martín. University Of Wisconsin; Estados Unidos Fil: Masneuf Pomarede, Isabelle. Bordeaux Sciences agro; Francia Fil: Albertin, Warren. Universite de Bordeaux; Francia Fil: Durrens, Pascal. Universite de Bordeaux; Francia Fil: Sherman, David James. Universite de Bordeaux; Francia Fil: Marullo, Philippe. Universite de Bordeaux; Francia. BIOLAFFORT; Francia Fil: Hittinger, Chris Todd. University Of Wisconsin; Estados Unidos Fil: Gonçalves, Paula. Universidade Nova de Lisboa; Portugal Fil: Sampaio, José Paulo . Universidade Nova de Lisboa; Portugal
Published: 2014
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18. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite

Author: Pascal Durrens, Adrien Zimmer, Cécile Durand, Nicolás Loira, Philippe Marullo, David James Sherman, Laffort [Floirac], Institut de Veille Sanitaire (INVS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Faculté d'Oenologie [Bordeaux II], Université Bordeaux Segalen - Bordeaux 2-Institut des Sciences de la Vigne et du Vin (ISVV), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Candidate gene, Saccharomyces cerevisiae Proteins, Heredity, quantitative genetics, Saccharomyces cerevisiae, Quantitative Trait Loci, lcsh:Medicine, Chromosomal translocation, Wine, Yeast and Fungal Models, Biology, Quantitative trait locus, Microbiology, polymorphisme génétique, Chromosomal Disorders, Model Organisms, vitis vinifera, Genetics, vin, saccharomyces cerevisiae, lcsh:Science, Gene, Fermentation in winemaking, Evolutionary Biology, Multidisciplinary, fermentation alcoolique, Quantitative Traits, qtl, lcsh:R, food and beverages, Human Genetics, Genomics, biology.organism_classification, Trait Locus, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Yeast, genome sequencing, Yeast in winemaking, oenologie, Fermentation, Translocations, oenology, lcsh:Q, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Research Article, Biotechnology
Abstract: International audience; Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI) involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity.
Published: 2014
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19. Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome ofSaccharomyces cerevisiaerevisited

Author: Bernard Dujon, Arnaud Perrin, Micheline Wésolowski-Louvel, Emmanuel Talla, Elisabeth Bon, Monique Bolotin-Fukuhara, Claire Toffano-Nioche, Jacky de Montigny, Serge Casaregola, Odile Ozier-Kalogeropoulos, Michel Aigle, Gaëlle Blandin, Jean-Luc Souciet, Serge Potier, Cécile Neuvéglise, Fredj Tekaia, Christian Marck, Bertrand Llorente, Claude Gaillardin, Andrée Lépingle, Alain Malpertuy, Pascal Durrens, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Microbiologie et Génétique Moléculaire (MGM), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-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), Unité de Microbiologie et génétique (UMG), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), 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, Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, Sequence analysis, Annotation, Genes, Fungal, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Intron, Saccharomyces cerevisiae, Biophysics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biochemistry, Genome, Open Reading Frames, Pseudogene, 03 medical and health sciences, Ascomycota, RNA, Transfer, Structural Biology, Genetics, Family, Frameshift, Molecular Biology, Gene, 030304 developmental biology, Sequence (medicine), 0303 health sciences, biology, 030302 biochemistry & molecular biology, Cell Biology, biology.organism_classification, Multigene Family, Transfer RNA, DNA, Intergenic, Chromosomes, Fungal, Genome, Fungal, Sequence Alignment
Abstract: International audience; Since its completion more than 4 years ago, the sequence of Saccharomyces cerevisiae has been extensively used and studied. The original sequence has received a few corrections, and the identification of genes has been completed, thanks in particular to transcriptome analyses and to specialized studies on introns, tRNA genes, transposons or multigene families. In order to undertake the extensive comparative sequence analysis of this program, we have entirely revisited the S. cerevisiae sequence using the same criteria for all 16 chromosomes and taking into account publicly available annotations for genes and elements that cannot be predicted. Comparison with the other yeast species of this program indicates the existence of 50 novel genes in segments previously considered as ‘intergenic’ and suggests extensions for 26 of the previously annotated genes.
Published: 2000
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20. 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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21. 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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22. A network of proteins around Rvs167p and Rvs161p, two proteins related to the yeast actin cytoskeleton

Author: Pascal Durrens, Elisabeth Bon, Masayuki Iwase, Akio Toh-e, Patricia Recordon-Navarro, and Michel Aigle
Subjects: Saccharomyces cerevisiae Proteins, Genetic Vectors, Saccharomyces cerevisiae, Bioengineering, Endocytosis, Applied Microbiology and Biotechnology, Biochemistry, Fungal Proteins, Open Reading Frames, Two-Hybrid System Techniques, Genetics, ORFS, Chromosomes, Artificial, Yeast, Cytoskeleton, Actin, Binding Sites, biology, Microfilament Proteins, Actin cytoskeleton, biology.organism_classification, Actins, Yeast, Cell biology, Cytoskeletal Proteins, Protein Binding, Biotechnology
Abstract: The Rvs161p and Rvs167p proteins of Saccharomyces cerevisiae, homologues of higher eukaryotes' amphiphysins, associate with actin and appear to be involved in several functions related to the actin cytoskeleton. In order to identify partners of the Rvsp proteins, yeast libraries constructed in two-hybrid vectors were screened using either Rvs167p or Rvs161p as a bait. The selected candidates, representing 34 ORFs, were then tested against both Rvsp proteins, as well as domains of Rvs167p or Rvs161p. Among the most significant ones, 24 ORFs were specific preys of Rvs167p only and two gave interactions with Rvs161p only. Interestingly, five ORFs were preys of both Rvs161p and Rvs167p (RVS167, LAS17, YNL094w, YMR192w and YPL249c). Analysis of putative functions of the candidates confirm involvement of the Rvsp in endocytosis/vesicle traffic, but also opens possible new fields, such as nuclear functions. Copyright © 2000 John Wiley & Sons, Ltd.
Published: 2000
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23. Protein–protein interaction between the RVS161 and RVS167 gene products of Saccharomyces cerevisiae

Author: Michel Aigle, Patricia Navarro, and Pascal Durrens
Subjects: Saccharomyces cerevisiae Proteins, Protein Conformation, Blotting, Western, Saccharomyces cerevisiae, Biophysics, Biochemistry, Protein Structure, Secondary, Protein–protein interaction, Fungal Proteins, Protein structure, Genes, Reporter, Structural Biology, Cytoskeleton, Molecular Biology, Gene, biology, Chemistry, Microfilament Proteins, Microfilament Protein, beta-Galactosidase, biology.organism_classification, Precipitin Tests, Blot, Cytoskeletal Proteins, Dimerization, Function (biology), Plasmids
Abstract: As previous studies indicated that the RVS161 and RVS167 gene products of Saccharomyces cerevisiae seem to be involved in the same cellular function, we considered the possibility of a complex between the proteins encoded by these two genes. Using the two hybrid system, we have shown that Rvs167p interacts with Rvs161p, through its N-terminal domain which contains predicted coiled-coil structures. Moreover, if a tagged Rvs 167p protein was immuno adsorbed under non-denaturing conditions, it brought along the Rvs161p protein. These results confirmed the hypothesis of an in vivo complex between the two proteins.
Published: 1997
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24. Comparative genomics of emerging pathogens in the Candida glabrata clade

Author: Christiane Bouchier, Christian Marck, Ralitsa Atanasova, Gabriela Aguileta, Adela Enache-Angoulvant, Toni Gabaldón, Eric Westhof, Cécile Fairhead, Bernard Dujon, Cécile Neuvéglise, Patrick Wincker, Marina Marcet-Houben, Tiphaine Martin, Arnaud Couloux, Laurence Ma, Julien Recoquillay, Eric Pelletier, Olivier Lespinet, Juliette Guitard, Julie Poulain, Sophie Creno, Hugo Devillers, Sylvie Arnaise, Stéphanie Boisnard, Amélie Pinard, José Almeida Cruz, Laure Jaouen, Monique Bolotin-Fukuhara, Christophe Hennequin, Pascal Durrens, Bioinformatics and Genomics Programme, Universitat Pompeu Fabra [Barcelona] (UPF)-Centre for Genomic Regulation (CRG), Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Immunité et Infection, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), 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), Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Comparative Genomics Group, CRG-Centre for Genomic Regulation, Service de Microbiologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Bicêtre, Institut de Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007- 2013)/ERC Grant Agreement n.310325, a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). CF's research is funded in part by an 'Attractivité' grant from the University Paris Sud. GA is a recipient of a Marie Curie grant (FP7-PEOPLE-2010-IEF-No.274223). SB, HD and RA are recipients of, respectively, a shared post-doctoral grant and a Ph. D. grant, from the Région Ile-de-France's DIM Malinf program. JAC was supported by the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/ BD/33528/2008)., European Project: 310325,NONCODEVOL - FP7-IDEAS-ERC, European Project: 274223,EC:FP7:PEOPLE,FP7-PEOPLE-2010-IEF,FUNGI-PATHNCODE(2012), Guitard, Juliette, Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hôpital Bicêtre, Mucoviscidose: physiopathologie et phénogénomique [CRSA], Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Parasitologie - Mycologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut Pasteur [Paris], Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Universitat Pompeu Fabra [Barcelona]-Centre for Genomic Regulation (CRG), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR113-Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique (Plate-Forme), Centre National de la Recherche Scientifique (CNRS)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Bicêtre, Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), BMC, Ed., Evolutionary genomics of long, non-coding RNAs - NONCODEVOL - FP7-IDEAS-ERC - 310325 - INCOMING, and The genomic basis of emerging fungal pathogenicity - FUNGI-PATHNCODE - - EC:FP7:PEOPLE2012-01-01 - 2013-12-31 - 274223 - VALID
Subjects: Nakaseomyces, Yeast evolution, [SDV]Life Sciences [q-bio], Yeast genomes, Virulence, Genomics, Candida glabrata, Genome, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene family, Selection, Genetic, Clade, DNA, Fungal, Phylogeny, Fungal pathogens, 030304 developmental biology, Comparative genomics, 0303 health sciences, biology, 030306 microbiology, Càndida, Llevats -- Genètica, Sequence Analysis, DNA, biology.organism_classification, 3. Good health, [SDV] Life Sciences [q-bio], Genòmica, Saccharomycetales, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genome, Fungal, Biotechnology, Research Article
Abstract: BACKGROUND: Candida glabrata follows C. albicans as the second or third most prevalent cause of candidemia worldwide. These two pathogenic yeasts are distantly related, C. glabrata being part of the Nakaseomyces, a group more closely related to Saccharomyces cerevisiae. Although C. glabrata was thought to be the only pathogenic Nakaseomyces, two new pathogens have recently been described within this group: C. nivariensis and C. bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts. RESULTS: Our results indicate that the two new pathogens are more closely related to the non-pathogenic N. delphensis than to C. glabrata. We uncover duplications and accelerated evolution that specifically affected genes in the lineage preceding the group containing N. delphensis and the three pathogens, which may provide clues to the higher propensity of this group to infect humans. Finally, the number of Epa-like adhesins is specifically enriched in the pathogens, particularly in C. glabrata. CONCLUSIONS: Remarkably, some features thought to be the result of adaptation of C. glabrata to a pathogenic lifestyle, are present throughout the Nakaseomyces, indicating these are rather ancient adaptations to other environments. Phylogeny suggests that human pathogenesis evolved several times, independently within the clade. The expansion of the EPA gene family in pathogens establishes an evolutionary link between adhesion and virulence phenotypes. Our analyses thus shed light onto the relationships between virulence and the recent genomic changes that occurred within the Nakaseomyces. This work was supported by funding from the European Research Council/nunder the European Union’s Seventh Framework Programme (FP/2007- 2013)/ERC Grant Agreement n.310325, a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). CF’s research is/nfunded in part by an “Attractivité” grant from the University Paris Sud. GA is/na recipient of a Marie Curie grant (FP7-PEOPLE-2010-IEF-No.274223). SB, HD and RA are recipients of, respectively, a shared post-doctoral grant and a Ph. D. grant, from the Région Ile-de-France’s DIM Malinf program. JAC was supported by the Ph.D. Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008)
Published: 2013
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25. The family based variability in protein family expansion

Author: Macha Nikolski, Pascal Durrens, Anasua Sarkar, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Information Technology [GCELT], Govt. College of Engineering and Leather Technology, plafrim, Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Protein family, sequence profiles, Clinical Biochemistry, Biomedical Engineering, Health Informatics, Computational biology, Biology, gene sequences, Genome, alignment selection criteria, 03 medical and health sciences, Health Information Management, optimal filtering strategy, ROC analysis, protein families, 030304 developmental biology, Genetics, 0303 health sciences, 030302 biochemistry & molecular biology, Computational Biology, remote homologues, bioinformatics, protein specific scoring matrix, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], proteins, ROC Curve, protein family expansion, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Family based, Algorithms
Abstract: International audience; In this paper we propose an automatic protein family expansion approach for recruitment of new members among the protein-coding genes in newly sequenced genomes. The criteria for adding a new member to a family depends on the structure of each individual family versus being globally uniform. The detection of a threshold in the ROC space of all sorted iterative profile sets defines the alignments selection criteria for each family. Furthermore, the statistical estimation of most-frequent optimal sorting criteria generates the optimal filtering strategy in a learning-parameter set for profile-based homology search.
Published: 2013
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26. Evidence for a branched pathway in the polarized cell division of Saccharomyces cerevisiae

Author: Pascal Durrens, E. Revardel, M. Bonneu, and Michel Aigle
Subjects: Genetics, Mutation, Mating type, Models, Genetic, Cell division, biology, Genes, Fungal, Mutant, Saccharomyces cerevisiae, Cell Polarity, Epistasis, Genetic, General Medicine, Genes, Mating Type, Fungal, medicine.disease_cause, biology.organism_classification, Phenotype, Fungal Proteins, medicine, Epistasis, Gene, Cell Division
Abstract: Cells of Saccharomyces cerevisiae can choose a bud site in one of two different spatial patterns (axial or bipolar) determined by their mating type. Genes important for bud-site selection have been identified and a linear model describing the hierarchy of these genes was proposed. We have uncovered a new class of genes which is required only for the bipolar pattern. The phenotype of the corresponding mutants coupled with epistasis experiments with some budding mutants already described suggest the existence of specific genes for the bipolar pathway.
Published: 1995
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27. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

Author: Joseph Schacherer, Patrick Wincker, Emmanuel Talla, Jean Weissenbach, Benoit Vacherie, Valérie Barbe, Marie Laure Straub, Philippe Baret, Stéphanie Weiss, Christine Sacerdot, Guillaume Morel, Jacky de Montigny, Eric Pelletier, José Almeida Cruz, Julie Poulain, Sandrine Mallet, Laurence Despons, Gaelle Samson, Serge Casaregola, Guilhem Savel, Guy-Franck Richard, Zlatyo Uzunov, Véronique Leh Louis, Valérie Kugler, Noémie Jacques, Marc Lemaire, David James Sherman, Agnès Thierry, Tiphaine Martin, Claude Gaillardin, Anasua Sarkar, Marie Line Seret, Anne Friedrich, Eric Westhof, Paul P. Jung, Cécile Fairhead, Cécile Neuvéglise, Pascal Durrens, Claudine Bleykasten, Christian Marck, Bernard Dujon, Jean Luc Souciet, Claire Jubin, Université de Strasbourg (UNISTRA), Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, AgroParisTech, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Architecture et Réactivité de l'ARN (ARN), Centre National de la Recherche Scientifique (CNRS)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Biologie systémique - Systems Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), 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)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-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), 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, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de Génomique d'Evry (IG), 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)-Direction de Recherche Fondamentale (CEA) (DRF (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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Strasbourg - UMR 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computer framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program 'Génotypage et Génomique Comparée,' and the ACI IMPBIO 'Génolevures En Ligne.'We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008), ANR-05-BLAN-0331,GENARISE,How do genes arise ? Lessons and questions from the evolution of yeast genomes.(2005), UCL - SST/ELI/ELIA - Agronomy, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université Catholique de Louvain = Catholic University of Louvain (UCL), 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-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 d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-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), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Genome evolution, Biology, Investigations, genome evolution, HEMIASCOMYCETOUS YEASTS, Gene dosage, Genome, allopolyploidy, Loss of heterozygosity, SACCHAROMYCES-CEREVISIAE, 03 medical and health sciences, NUCLEOLAR DOMINANCE, CANDIDA-ALBICANS, DNA-SEQUENCES, EVOLUTION, GENE, GLYCEROL, HALOTOLERANT, SPECIATION, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene duplication, Genetics, Molecular Biology, Gene, hybridization, Genetics (clinical), [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, osmotolerant yeast P. sorbitophila, osmotolerant yeast P, Numt, loss of heterozygosity, GC-content
Abstract: the Consortium National de Recherche en Génomique (CNRG) to Génoscope, CNRS (GDR 2354, Génolevures), The computer framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program "Génotypage et Génomique Comparée," and the ACI IMPBIO "Génolevures En Ligne."; International audience; Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
Published: 2012
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28. Rapid Discrimination between Candida glabrata, Candida nivariensis, and Candida bracarensis by Use of a Singleplex PCR ▿

Author: Pascal Durrens, Cécile Fairhead, Juliette Guitard, Tiphaine Martin, Christophe Hennequin, Adela Enache-Angoulvant, Frédéric Grenouillet, Mucoviscidose: physiopathologie et phénogénomique [CRSA], Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Parasitologie - Mycologie [CHU Saint-Antoine], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre de Physique Théorique - UMR 6207 (CPT), Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-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), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), 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), Hôpital Bicêtre, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Immunité et Infection, IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Laboratoire de Parasitologie-Mycologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Mycology-Parasitology Department, Université de Franche-Comté (UFC), Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Guitard, Juliette, Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Service Parasitologie-Mycologie, Hôpital St. Antoine, Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR113-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Université de Franche-Comté ( UFC ), Models and Algorithms for the Genome ( MAGNOME ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), ( MABIOVIS ), 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 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 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, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR113-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: Microbiology (medical), Microbiological Techniques, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Mycology, Biology, Polymerase Chain Reaction, Microbiology, 03 medical and health sciences, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, DNA, Ribosomal Spacer, Humans, Base sequence, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, DNA, Fungal, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Candida bracarensis, 030304 developmental biology, Candida, DNA Primers, 0303 health sciences, Candida glabrata, Base Sequence, 030306 microbiology, Fungal genetics, Candidiasis, Sequence Analysis, DNA, Amplicon, biology.organism_classification, Candida nivariensis, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Primer (molecular biology), Sequence Alignment, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: We report here a PCR-based assay using a single primer pair targeting the RPL31 gene that allows discrimination between Candida glabrata , Candida bracarensis , and Candida nivariensis according to the size of the generated amplicon.
Published: 2011
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29. How does Oenococcus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock

Author: Aurélie Goulielmakis, Julen Bridier, Aurélien Barré, Olivier Claisse, David James Sherman, Pascal Durrens, Aline Lonvaud-Funel, Elisabeth Bon, Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Unité de Recherche Oenologie [Villenave d'Ornon], Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV), CBiB-Centre de Bioinformatique de Bordeaux, Université Bordeaux Segalen - Bordeaux 2, Univ. Bordeaux Segalen (P. Darriet, L. Geny, P. Lucas, A. Lonvaud, G. de Revel, P.L. Teissedre), DIVOENI, Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), 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 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, Bon, Elisabeth, Univ. Bordeaux Segalen (P. Darriet, L. Geny, P. Lucas, A. Lonvaud, G. de Revel, P.L. Teissedre), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Œnologie, and Institut National de la Recherche Agronomique (INRA)-Université Victor Segalen - Bordeaux 2
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: ISBN : 9782100575961; International audience; Oenococcus oeni is a small lactic acid bacterium with a compact genome (~ 2 Mb in size and ca. 1800 genes) that is naturally found in oenological and coder niches, and is the most common agent associated with malolactic fermentation (MLF). The diversity of metabolisms and adaptations to the environment of this species renders MLF quite unpredictable. Until now, the understanding of how O. oeni adapts to its niche has been treated through a classical genomic-phenotypic angle, and has revealed the role of genome plasticity (local mutations; differential gene insertion-deletions) in these adaptations. In this work, we endeavored to elucidate this dialogue between genes and environment, by exploring how the expression system is solicited when O. oeni strains are placed under stress-exposure conditions.
Published: 2011

30. The Génolevures database

Author: David James Sherman, Pascal Durrens, Tiphaine Martin, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-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)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Computer science, Molecular Sequence Data, computer.software_genre, Genome, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Access to Information, 03 medical and health sciences, Annotation, Ascomycota, Databases, Genetic, Saccharomycotina, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Internet, 0303 health sciences, Base Sequence, General Immunology and Microbiology, Database, biology, Computers, business.industry, 030302 biochemistry & molecular biology, Online database, General Medicine, Genome project, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Logical relations, The Internet, Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], General Agricultural and Biological Sciences, business, computer
Abstract: The Génolevures online database (URL: http://www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several campaigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedicated to large-scale comparison of these genomes, storing not only the different chromosomal elements detected in the sequences, but also the logical relations between them. The database is divided into a public part, accessible to anyone through Internet, and a private part where the Consortium members make genome annotations with our Magus annotation system; this system is used to annotate several related genomes in parallel. The public database is widely consulted and offers structured data, organized using a REST web site architecture that allows for automated requests. The implementation of the database, as well as its associated tools and methods, is evolving to cope with the influx of genome sequences produced by Next Generation Sequencing (NGS).
Published: 2011
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31. The Génolevures website comparative genomic studies on hemiascomycetous yeasts

Author: Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens, Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), CNRS (GDR 2354 : Génolevures,INS2I, INSB) région Aquitain ('Pôle de Recherche en informatique')(2005-1306001AB, partie, 2010l) ACI IMPBIO (IMPB114, 'Génolevures En Ligne'), EMBL-EMBO, ANR-05-BLAN-0033,CASDOA,Caractérisation Astronomique du Site du Dôme C en Antarctique(2005), Martin, Tiphaine, Programme non thématique - Appel à projets de recherche - Caractérisation Astronomique du Site du Dôme C en Antarctique - - CASDOA2005 - ANR-05-BLAN-0033 - BLANC - VALID, Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-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: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; The Génolevures website (http://cbi.labri.fr/Genolevures/ or http://genolevures.org/) provides tools and data relative to complete, partial, and mitochondrial genome sequences from 31 species of hemiascomycetes yeasts to facilitate comparative genomics studies of this clade. These sequences are manually annotated and regularly updated by a network of practicing experimental biologists from the Génolevures Consortium. Moreover, the Génolevures website has the benefit of continuous progress thanks to the constant addition of new annotated genomes, novel studies and new tools. The tools and data on the Génolevures website are organised around the typical questions of molecular evolution asked by biologists, such as the degree of gene conservation, the identification of species-specific, clade-specific or class-specific genes, the distribution of genes among functional families, and mechanisms of chromosome shuffling (cf.figure 1). Figure 1: The Génolevurs website : its tools and data (October 2009) All data from the Génolevures website are freely available, and instructions for proper citation are included in each section. The Génolevures website is developed using a ‘representational state transfer' architecture and URLs for individual identified resources built from the database can be constructed systematically.
Published: 2009

32. Oenococcus oeni genome plasticity associated with adaptation to wine, an extreme ecological niche

Author: Elisabeth Bon, Arnaud Delaherche, Eric Bilhere, Cécile MIOT-SERTIER, Pascal Durrens, Antoine de Daruvar, Aline Lonvaud-Funel, Claire Le Marrec, Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institut des Sciences de la Vigne et du Vin (ISVV), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Biotechnologie et Microbiologie Appliquée (LBMA), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Eric Rivals and Irena Rusu, 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 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, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Bon, Elisabeth
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience
Published: 2009

33. Base de données Génolevures : génomique comparative des Hemiascomycetes

Author: Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), CNRS (GDR 2354 : Génolevures) région Aquitain ('Pôle de Recherche en informatique')(2005-1306001AB, partiel) ACI IMPBIO (IMPB114, 'Génolevures En Ligne'), Eric Rivals and Irena Rusu, ANR-05-BLAN-0033,CASDOA,Caractérisation Astronomique du Site du Dôme C en Antarctique(2005), Martin, Tiphaine, Programme non thématique - Appel à projets de recherche - Caractérisation Astronomique du Site du Dôme C en Antarctique - - CASDOA2005 - ANR-05-BLAN-0033 - BLANC - VALID, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), 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 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 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, GENARISE, ANR-05-BLAN-033,GENARISE, ANR-05-BLAN-033, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-WB] Computer Science [cs]/Web, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [INFO.INFO-WB]Computer Science [cs]/Web, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience
Published: 2009

34. The Génolevures online database

Author: Tiphaine Martin, Macha Nikolski, David James Sherman, Jean-Luc Souciet, Pascal Durrens, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), GDR 2354 Génolevures ACI IMPBIo, IMPB114,Génolevures En Ligne Région Aquitaine (‘Pôle de Recherche en Informatique') (2005-1306001AB), ANR-05-BLAN-0331,GENARISE,How do genes arise ? Lessons and questions from the evolution of yeast genomes.(2005), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Martin, Tiphaine, and Programme non thématique - Appel à projets de recherche - How do genes arise ? Lessons and questions from the evolution of yeast genomes. - - GENARISE2005 - ANR-05-BLAN-0331 - BLANC - VALID
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience
Published: 2009

35. Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes

Author: David J, Sherman, Tiphaine, Martin, Macha, Nikolski, Cyril, Cayla, Jean-Luc, Souciet, Pascal, Durrens, E, Westhof, Models and Algorithms for the Genome (MAGNOME), INRIA Futurs, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-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), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), 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, and 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 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
Subjects: Proteome, Protein family, In silico, Genomics, Biology, Synteny, Genome, Fungal Proteins, 03 medical and health sciences, Ascomycota, Yeasts, Databases, Genetic, Genetics, 030304 developmental biology, 0303 health sciences, Fungal protein, 030302 biochemistry & molecular biology, Articles, Subtelomere, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gene Fusion, Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; The Genolevures online database (http://cbi.labri.fr/Genolevures/ and http://genolevures.org/) provides exploratory tools and curated data sets relative to nine complete and seven partial genome sequences determined and manually annotated by the Genolevures Consortium, to facilitate comparative genomic studies of Hemiascomycete yeasts. The 2008 update to the Genolevures database provides four new genomes in complete (subtelomere to subtelomere) chromosome sequences, 50 000 protein-coding and tRNA genes, and in silico analyses for each gene element. A key element is a novel classification of conserved multi-species protein families and their use in detecting synteny, gene fusions and other aspects of genome remodeling in evolution. Our purpose is to release high-quality curated data from complete genomes, with a focus on the relations between genes, genomes and proteins.
Published: 2009
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36. The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeasts

Author: Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, David James Sherman, Jean-Luc Souciet, Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Martin, Tiphaine, Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-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: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience
Published: 2008

37. Gene Fusion and Fission Events in Fungal Genomes

Author: Pascal Durrens, Macha Nikolski, David James Sherman, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Models and Algorithms for the Genome (MAGNOME), INRIA Futurs, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), ANR-05-BLAN-0331,GENARISE,How do genes arise ? Lessons and questions from the evolution of yeast genomes.(2005), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Sherman, David James, and Programme non thématique - Appel à projets de recherche - How do genes arise ? Lessons and questions from the evolution of yeast genomes. - - GENARISE2005 - ANR-05-BLAN-0331 - BLANC - VALID
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience
Published: 2007

38. The Génolevures online database

Author: Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, David James Sherman, Jean-Luc Souciet, Models and Algorithms for the Genome (MAGNOME), INRIA Futurs, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), CNRS (GDR 2354 : Génolevures) region Aquitaine ('Pôle de Recherche en Informatique')(2005-1306001AB, partiel) ACI IMPBIO (IMPB114, 'Génolevures En Ligne'), J.Micheal Cherry and Ian G. Macreadie, 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 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 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, Martin, Tiphaine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-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: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience
Published: 2007

39. Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cerevisiae strains

Author: Gaël Yvert, Isabelle Masneuf-Pomarède, Pascal Durrens, Denis Dubourdieu, Michel Aigle, Philippe Marullo, Marina Bely, Faculté d'Oenologie [Bordeaux II], Université Bordeaux Segalen - Bordeaux 2-Institut des Sciences de la Vigne et du Vin (ISVV), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Models and Algorithms for the Genome (MAGNOME), INRIA Futurs, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire de la cellule ( BMC ), École normale supérieure - Lyon ( ENS Lyon ) -Institut National de la Recherche Agronomique ( INRA ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Models and Algorithms for the Genome ( MAGNOME ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique ( CNRS ), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Nonsynonymous substitution, QTL mapping, Saccharomyces cerevisiae Proteins, Nitrogen, Saccharomyces cerevisiae, Quantitative Trait Loci, Wine, Quantitative trait locus, Applied Microbiology and Biotechnology, Microbiology, Genome, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genotype, Asparaginase, Pyrophosphatases, 030304 developmental biology, Acetic Acid, 2. Zero hunger, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, 030306 microbiology, DNA microarray, Chromosome Mapping, Reproducibility of Results, General Medicine, Quantitative genetics, Carbon Dioxide, biology.organism_classification, ASP1, Aneuploidy, Yeast, wine fermentation, Phenotype, Chromosomes, Fungal, Genome, Fungal, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract: International audience; Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. However, the link between phenotype variation and genetic determinism is still difficult to identify, especially in wild populations. Using genome hybridization on DNA microarrays, it is now possible to identify single-feature polymorphisms among divergent yeast strains. This tool offers the possibility of applying quantitative genetics to wild yeast strains. In this instance, we studied the genetic basis for variations in acetic acid production using progeny derived from two strains from grape must isolates. The trait was quantified during alcoholic fermentation of the two strains and 108 segregants derived from their crossing. A genetic map of 2212 markers was generated using oligonucleotide microarrays, and a major quantitative trait locus (QTL) was mapped with high significance. Further investigations showed that this QTL was due to a nonsynonymous single-nucleotide polymorphism that targeted the catalytic core of asparaginase type I (ASP1) and abolished its activity. This QTL was only effective when asparagine was used as a major nitrogen source. Our results link nitrogen assimilation and CO(2) production rate to acetic acid production, as well as, on a broader scale, illustrating the specific problem of quantitative genetics when working with nonlaboratory microorganisms.
Published: 2007
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40. A novel link between a Rab GTPase and Rvs proteins: the yeast amphiphysin homologues

Author: Michel Aigle, Nicolas Talarek, Axelle Balguerie, Pascal Durrens, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Unité de Microbiologie et génétique (UMG), 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), and Université de Lyon
Subjects: Saccharomyces cerevisiae Proteins, Molecular Sequence Data, Clinical Biochemistry, Mutant, Saccharomyces cerevisiae, Fus2p, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], GTPase, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Biochemistry, SH3 domain, src Homology Domains, 03 medical and health sciences, 0302 clinical medicine, Two-Hybrid System Techniques, GAP protein (Gyp5p, Ymr192p), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Vesicular traffic, Cytokinesis, 030304 developmental biology, Genetics, 0303 health sciences, Sequence Homology, Amino Acid, Microfilament Proteins, Cell Biology, General Medicine, biology.organism_classification, Fusion protein, Cell biology, Rvsp, rab GTP-Binding Proteins, Amphiphysin, Rab, 030217 neurology & neurosurgery
Abstract: The BAR proteins are a well-conserved family of proteins including Rvsp in yeast, amphiphysins and Bin proteins in mammals. In yeast, as in mammals, BAR proteins are known to be implicated in vesicular traffic. The Gyp5p (Ypl249p) and Ymr192p proteins interact in two-hybrid tests with both Rvs161p and Rvs167p. Gyp5p is a Ypt/Rab-specific GAP and Ymr192p is highly similar to Gyp5p. To specify the interaction between Rvsp and Gyp5p, we used two-hybrid tests to determine the domains necessary for these interactions. The specific SH3 domain of Rvs167p interacted with the N-terminal domain of Gyp5p. Moreover, Gyp5p could form a homodimer. Fus2 protein is a specific partner of Rvs161p in two-hybrid tests. To characterize the functional relationships between these five proteins, we have studied cellular phenotypes in single, double and triple mutant strains for which rvs mutants present defects, such as polarity, cell fusion and meiosis. Phenotypic analysis showed that Gyp5p, Ymr192p and Fus2p were involved in bipolar budding pattern and in meiosis. Specific epistasis or suppressive phenomena were found between the five mutations. Finally, The Gyp5p–GFP fusion protein was localized at the bud tip during apical growth and at the mother-bud neck during cytokinesis. Moreover, Rvs167p and Rvs161p were shown to be essential for the correct localization of Gyp5p. Altogether, these data support the hypothesis that both Rvsp proteins act in vesicular traffic through physical and functional interactions with Ypt/Rab regulators. Copyright © 2004 John Wiley & Sons, Ltd.
Published: 2005
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41. Genome evolution in yeasts

Author: Valérie Barbe, Laurence Cattolico, Isabelle Lesur, Alix Kerrest, Hélène Ferry-Dumazet, Fabrice Confanioleri, Serge Casaregola, Emmanuel Talla, Véronique Anthouard, Jean-Marie Beckerich, Laurence Ma, Odile Ozier-Kalogeropoulos, Nicolas Jauniaux, Nicolas Goffard, Jacky de Montigny, David James Sherman, Antoine de Daruvar, Serge Potier, Guy-Franck Richard, Romain Koszul, Pascal Durrens, Anna Babour, Sophie Oztas, Emmanuelle Beyne, Christian Marck, Patrick Wincker, Emmanuelle Fabre, Stefan Pellenz, Bernard Dujon, Florence Hantraye, Eric Westhof, Cécile Fairhead, Micheline Wésolowski-Louvel, Cécile Neuvéglise, Gilles Fischer, Laurence Despons, Christophe Hennequin, Jean Weissenbach, Marie-Laure Straub, Audrey Suleau, Stéphanie Barnay, Jean-Marc Nicaud, Macha Nikolski, Claude Gaillardin, Claudine Bleykasten, Jean-Luc Souciet, Fredj Tekaia, Philippe Joyet, Rym Kachouri, Sylvie Blanchin, Bénédicte Wirth, Héloïse Muller, Christiane Bouchier, Maria Zeniou-Meyer, Ingrid Lafontaine, Jeanne Boyer, Monique Bolotin-Fukuhara, Ivan Zivanovic, Claude Scarpelli, Bernard Caudron, Agnès Thierry, Dominique Swennen, Alexis Groppi, Anita Boisramé, Michel Aigle, Lionel Frangeul, Marc Lemaire, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Collection de Levures d'Intérêt Biotechnologique et Laboratoire de Génétique Moléculaire et Cellulaire, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamique, évolution et expression de génomes de microorganismes (DEEGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Service de Biochimie, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), 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), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique des Interactions Macromoléculaires, Institut Pasteur [Paris] (IP)-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), Architecture et réactivité de l'ARN (ARN), Logiciels et Banques de Données, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), 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, Génomique (Plate-Forme), Institut Pasteur [Paris], Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris]-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: MESH: Tandem Re, MESH: Research Support, Non-U.S. Gov't, Genome, MESH: Saccharomyces cerevisiae Proteins, RNA, Transfer, Gene Duplication, Yeasts, Conserved Sequence, MESH: Evolution, Molecular, Segmental duplication, Genomic organization, Genetics, SACCHAROMYCES CEREVISIAE, 0303 health sciences, Multidisciplinary, MESH: Conserved Sequence, MESH: Yeasts, MESH: Gene Duplication, MESH: Synteny, Genome project, MESH: Chromosomes, Fungal, Tandem Repeat Sequences, MESH: Genome, Fungal, Chromosomes, Fungal, Genome, Fungal, GENETIC MAPPING, Genome evolution, Saccharomyces cerevisiae Proteins, Genes, Fungal, Molecular Sequence Data, Biology, Synteny, Evolution, Molecular, 03 medical and health sciences, GENOME ORGANIZATION, Molecular evolution, YEAST, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, Comparative genomics, STRUCTURE DU GENOME, MESH: Molecular Sequence Data, 030306 microbiology, MESH: RNA, Transfer, MOLECULAR EVOLUTION, MESH: Tandem Repeat Sequences, Evolutionary biology, RNA, Ribosomal, MESH: RNA, Ribosomal, MESH: Genes, Fungal
Abstract: Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
Published: 2004
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42. Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts

Author: Jean-Luc Souciet, Pascal Durrens, Emmanuelle Beyne, David James Sherman, Macha Nikolski, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and GDR CNRS 2354 'Génolevures'
Subjects: Information Storage and Retrieval, Genomics, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, Molecular evolution, Kluyveromyces, Yeasts, Databases, Genetic, Genetics, 030304 developmental biology, Synteny, Comparative genomics, Kluyveromyces lactis, 0303 health sciences, Internet, [SDV.GEN]Life Sciences [q-bio]/Genetics, 030306 microbiology, Computational Biology, Articles, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software, Reference genome
Abstract: International audience; The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides data and tools to facilitate comparative genomic studies on hemiascomycetous yeasts. Now, four complete genome sequences recently determined (Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica) have been added to the partial sequences of 13 species previously analysed by a random approach. The database also includes the reference genome Saccharomyces cerevisiae. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes a community area for specific studies by members of the international community.
Published: 2004
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43. HIV-1 integrase interacts with yeast microtubule-associated proteins

Author: Michel Fournier, Elisabeth Bon, Vincent Parissi, Christina Calmels, Vaea Richard de Soultrait, Pascal Durrens, Laura Tarrago-Litvak, Anne Caumont, Cécile Desjobert, and Patricia Recordon
Subjects: Microtubule-associated protein, Biophysics, HIV Integrase, Saccharomyces cerevisiae, Biology, Biochemistry, Spindle pole body, law.invention, Structural Biology, Microtubule, law, Genetics, Humans, Genomic library, Binding Sites, Molecular biology, Yeast, Recombinant Proteins, Cell biology, Integrase, genomic DNA, Recombinant DNA, biology.protein, HIV-1, Microtubule-Associated Proteins, Protein Binding
Abstract: The human immunodeficiency virus type 1 (HIV-1) integrase (IN) mediates the insertion of viral DNA into the human genome. In addition to IN, cellular and viral proteins are associated to proviral DNA in the so-called preintegration complex (PIC). We previously reported that the expression of HIV-1 IN in yeast leads to the emergence of a lethal phenotype. This effect may be linked to the IN activity on infected human cells where integration requires the cleavage of genomic DNA. To isolate and characterize potential cellular partners of HIV-1 IN, we used it as a bait in a two-hybrid system with a yeast genomic library. IN interacted with proteins belonging to the microtubule network, or involved in the protein synthesis apparatus. We focused our interest on one of the selected inserts, L2, which corresponds to the C-end half of the yeast STU2p, a microtubule-associated protein (MAP). STU2p is an essential component of the yeast spindle pole body (SPB), which is able to bind microtubules in vitro. After expressing and purifying L2 as a recombinant protein, we showed its binding to IN by ELISA immunodetection. L2 was also able to inhibit IN activity in vitro. In addition, the effect of L2 was tested using the “lethal yeast phenotype”. The coexpression of IN and the L2 peptide abolished the lethal phenotype, thus showing important in vivo interactions between IN and L2. The identification of components of the microtubule network associated with IN suggest a role of this complex in the transport of HIV-1 IN present in the PIC to the nucleus, as already described for other human viruses.
Published: 2002

44. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

Author: Rüdiger Bode, Martin Mascher, Serge Casaregola, Anasua Sarkar, Guilhem Savel, Patrick Wincker, Valérie Barbe, Martin Giersberg, Marina Marcet-Houben, Keith Baronian, Nils Stein, Véronique Leh-Louis, Christine Sacerdot, Guy-Franck Richard, Jan Riechen, Ingrid Lafontaine, Jean Luc Souciet, Urs Hähnel, Eric Westhof, Joseph Schacherer, Uwe Scholz, Sebastian Worch, Sebastian Beier, Pascal Durrens, Erik Böer, Anke Trautwein-Schult, Christian Marck, Toni Gabaldón, Cécile Fairhead, Anja Hartmann, Claire Jubin, Bernard Dujon, Cécile Neuvéglise, Małgorzata Czernicka, Claudine Bleykasten, David James Sherman, Laurence Despons, Marie Laure Straub, Paul P. Jung, Marc Lemaire, Dagmara Jankowska, Tiphaine Martin, Benoit Vacherie, Emmanuel Talla, Agnès Thierry, José Almeida Cruz, André Goffeau, Gotthard Kunze, Claude Gaillardin, Philippe Baret, Guillaume Morel, Przemysław Piotr Gierski, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Yeast Genetics, Leibniz Institute of Plant Research (IPK), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institute of Plant Biology and Biotechnology, University of Agriculture in Krakow, 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, Models and Algorithms for the Genome ( MAGNOME), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université catholique de Louvain, Institut des Sciences de la Vie, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), School of Biological Sciences, University of Canterbury, Institute of Biochemistry, Universität Greifswald - University of Greifswald, Université de Strasbourg (UNISTRA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Génétique moléculaire, génomique, microbiologie (GMGM), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire des levures (YMG), Microbiologie, adaptation et pathogénie (MAP), 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)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program ' Génotypage et Génomique Comparée ' , the ACI IMPBIO ' Génolevures En Ligne ' and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia, SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161)., Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Canterbury [Christchurch], International Institute of Molecular and Cell Biology [Warsaw] (IIMCB), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Kunze, Gotthard, Neuvéglise, Cécile, UCL - SST/ELI/ELIA - Agronomy, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: Yarrowia lipolytica, n-butanol, yeast, genome, tannic acid, metabolism, biotechnology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Technological development, Butyric acid, Applied Microbiology and Biotechnology, Genome, Blastobotrys, Saccharomycotina, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, N-butanol, 2. Zero hunger, 0303 health sciences, biology, Segmental duplications, Genomics, Phylogenetics, General Energy, Biochemistry, Biotechnology, Nitrogen, Saccharomyces cerevisiae, Biotecnologia agrícola, Computational biology, Management, Monitoring, Policy and Law, Biotechnological potentials, Arxula, Arxula adeninivorans, 03 medical and health sciences, Carbon and nitrogen, 030304 developmental biology, Saccharomycetes, Comparative genomics, Tannic acid, 030306 microbiology, Renewable Energy, Sustainability and the Environment, Protein, Research, Fundamental studies, Yarrowia, Llevats -- Genètica, biology.organism_classification, Yeast, Carbon, Metabolism, Genes, Organic acid
Abstract: Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant./nResults: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications. This work was supported in part by funding from the Consortium National de Recherche en Génomique (CNRG) to Génoscope, from CNRS (GDR 2354, Génolevures), ANR (ANR-05-BLAN-0331, GENARISE). The computing framework was supported by the funding of the University of Bordeaux 1, the Aquitaine Région in the program “Génotypage et Génomique Comparée”, the ACI IMPBIO “Génolevures En Ligne” and INRIA. We thank the System and Network Administration team in LaBRI for excellent help and advice. J.A.C. is supported by the PhD Program in Computational Biology of the Instituto Gulbenkian de Ciência, Portugal (sponsored by Fundação Calouste Gulbenkian, Siemens SA, and Fundação para a Ciência e Tecnologia; SFRH/BD/33528/2008). M.C. research was supported by a grant of the Deutscher Akademischer Austauschdienst (DAAD). T.G. research was partly supported by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161). B.D. is a member of Institut Universitaire de France
Published: 2014
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45. Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum

Author: Cécile Neuvéglise, François Artiguenave, Pascal Durrens, Elisabeth Bon, Serge Casaregola, Patrick Wincker, Michel Aigle, 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, Retroelements, Saccharomyces cerevisiae, Centromere, Molecular Sequence Data, Biophysics, Saccharomyces bayanus, Introgression, Translocation, Retrotransposon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Biochemistry, 03 medical and health sciences, Contig Mapping, Saccharomyces, Ascomycota, Structural Biology, Gene Order, Genetics, ORFS, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Synteny, 0303 health sciences, 030306 microbiology, Cell Biology, Sequence Analysis, DNA, Ty, biology.organism_classification, Open reading frame, Chromosomes, Fungal, Genome, Fungal
Abstract: Saccharomyces bayanus var. uvarum investigated here is the species closest to Saccharomyces cerevisiae. Random sequence tags (RSTs) allowed us to identify homologues to 2789 open reading frames (ORFs) in S. cerevisiae, ORFs duplicated in S. uvarum but not in S. cerevisiae, centromeres, tRNAs, homologues of Ty1/2 and Ty4 retrotransposons, and a complete rDNA repeat. Only 13 RSTs seem to be homologous to sequences in other organisms but not in S. cerevisiae. As the synteny between the two species is very high, cases in which synteny is lost suggest special mechanisms of genome evolution. The corresponding RSTs revealed that S. uvarum can exist without any S. cerevisiae DNA introgression. Accession numbers are from AL397139 to AL402278 in the EMBL databank.
Published: 2001

46. Evolution of gene order in the genomes of two related yeast species

Author: Bernard Dujon, Claude Gaillardin, Cécile Neuvéglise, Gilles Fischer, Pascal Durrens, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), and 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
Subjects: 0106 biological sciences, Genetic Linkage, Genes, Fungal, Molecular Sequence Data, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Saccharomyces bayanus, Saccharomyces cerevisiae, 01 natural sciences, Genome, Translocation, Genetic, Evolution, Molecular, Saccharomyces, 03 medical and health sciences, Gene Duplication, Gene Order, Gene duplication, Gene cluster, Genetics, Gene, Genetics (clinical), 030304 developmental biology, Synteny, Chromosomal inversion, Recombination, Genetic, 0303 health sciences, Concerted evolution, biology, biology.organism_classification, Chromosome Inversion, Chromosomes, Fungal, Genome, Fungal, Gene Deletion, 010606 plant biology & botany
Abstract: Changes in gene order between the genomes of two related yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum were studied. From the dataset of a previous low coverage sequencing of the S. bayanus var.uvarum genome, 35 different synteny breakpoints between neighboring genes and two cases of local gene inversion were characterized in detail. The number and the type of the chromosomal rearrangements that have lead to these differences were identified. We show that evolution of gene order in the genomes of these two yeast species is driven mainly by gene duplication onto different chromosomes followed by differential loss of the repeated copies. In addition, local gene inversions also would result from a mechanism of gene duplication, but in an inverted orientation, followed by loss of the original copy. The identification of traces of anciently duplicated genes, called relics, show that the loss of duplicates is more frequently caused by the accumulation of numerous mutations in one of the two copies than by DNA deletion. Surprisingly, gross chromosomal rearrangements such as translocations have only a minor effect on gene order reshuffling as they account for [The sequence data have been submitted to the EMBL Library under accession nos. AJ316068 and AJ316069.]
Published: 2001
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47. 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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48. Characterization of a new gene family developing pleiotropic phenotypes upon mutation in Saccharomyces cerevisiae

Author: Emmanuelle Revardel, Michel Aigle, Marc Bonneau, and Pascal Durrens
Subjects: Saccharomyces cerevisiae Proteins, Mutant, Genes, Fungal, Molecular Sequence Data, Biophysics, Pair-rule gene, Saccharomyces cerevisiae, Gene mutation, Biology, Biochemistry, Gene dosage, Fungal Proteins, Structural Biology, Gene cluster, Genetics, Gene family, Amino Acid Sequence, Gene, Base Sequence, Microfilament Proteins, Cortical actin cytoskeleton, Cytoskeletal Proteins, Phenotype, Mutation, Sequence Alignment
Abstract: The aim of this paper is to gather and complete data about four members of a new gene family. Mutation in SUR4 gene was originally selected as a suppressor of defects caused by mutations in RVS161 or RVS167 genes. Cloning and sequencing of the SUR4 gene were performed. The deduced protein contains six putative transmembrane domains. Sequence comparison revealed that two yeast genes, FEN1 and JO343, shared significant similarities with SUR4. Mutants for SUR4 and FEN1 have the same pleiotropic phenotype, including bud localization defects, resistance to an immunosuppressor and resistance to ergosterol biosynthesis inhibitors. The double inactivation of SUR4 and FEN1 genes is lethal. These data and other aspects implicating SUR4 in glucose metabolism, suggest an involvement of these genes in the dynamics of cortical actin cytoskeleton in response to nutrient availability. Moreover, the existence of a fourth homologous gene in C. elegans extends the family to pluricellular organisms.
Published: 1995

49. Yeast mutants affected in viability upon starvation have a modified phospholipid composition

Author: M. Bonneu, Michel Aigle, H. Juguelin, L. Desfarges, C. Cassagne, and Pascal Durrens
Subjects: Mutant, Saccharomyces cerevisiae, Genes, Fungal, Phospholipid, Bioengineering, Biology, medicine.disease_cause, Applied Microbiology and Biotechnology, Biochemistry, Biological pathway, chemistry.chemical_compound, Suppression, Genetic, Genetics, medicine, Gene, Crosses, Genetic, Phospholipids, Mutation, Genetic Complementation Test, biology.organism_classification, Yeast, Complementation, Phenotype, chemistry, Cell Division, Biotechnology
Abstract: Selection of mutations, based on the suppression of rvs161 delta defects, was performed. Ten mutants were obtained, ranged amongst four complementation groups, named SUR1, SUR2, SUR3 and SUR4. All sur mutations also suppress a mutation in another gene, RVS167, indicating that all six genes are involved in the same biological pathway. The sur mutant cells have abnormal morphologies in stationary phase, i.e. dumbbell-like in sur1, sur2 or sur3 strains and multi-budded in sur4 strains. Several phenotypic characteristics of the physiological suppressors as well as the rvs161 delta strain itself led us to analyse the phospholipid composition of the mutants. The assays show an overall decrease of the phospholipid amounts and modifications in the relative contents of some phospholipid classes in sur mutant cells.
Published: 1993

50. Genome-wide computational prediction of tandem gene arrays: application in yeasts

Author: Véronique Leh Louis, Pascal Durrens, Laurence Despons, Jean-Luc Souciet, Philippe Baret, Lionel Frangeul, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Catholique de Louvain = Catholic University of Louvain (UCL), Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Institut Pasteur [Paris], Models and Algorithms for the Genome ( MAGNOME), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), This work was supported in part by the Génolevures-3 sequencing consortium GDR 2354 from CNRS and by ANR-05-BLAN-0331 (GENARISE), Institut Pasteur [Paris] (IP), Inria Bordeaux - Sud-Ouest, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Sequence Analysis, DNA, lcsh:QH426-470, lcsh:Biotechnology, In silico, MESH: Algorithms, Minisatellite Repeats, Computational biology, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Protein sequencing, Yeasts, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], lcsh:TP248.13-248.65, Databases, Genetic, Genetics, Coding region, Gene conversion, MESH: Phylogeny, Gene, Phylogeny, MESH: Databases, Genetic, MESH: Evolution, Molecular, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Comparative genomics, 0303 health sciences, Methodology Article, MESH: Yeasts, MESH: Genomics, Computational Biology, Genomics, Sequence Analysis, DNA, lcsh:Genetics, MESH: Genome, Fungal, MESH: Minisatellite Repeats, MESH: Oligonucleotide Array Sequence Analysis, Genome, Fungal, DNA microarray, Algorithms, 030217 neurology & neurosurgery, MESH: Computational Biology, Biotechnology
Abstract: Background This paper describes an efficient in silico method for detecting tandem gene arrays (TGAs) in fully sequenced and compact genomes such as those of prokaryotes or unicellular eukaryotes. The originality of this method lies in the search of protein sequence similarities in the vicinity of each coding sequence, which allows the prediction of tandem duplicated gene copies independently of their functionality. Results Applied to nine hemiascomycete yeast genomes, this method predicts that 2% of the genes are involved in TGAs and gene relics are present in 11% of TGAs. The frequency of TGAs with degenerated gene copies means that a significant fraction of tandem duplicated genes follows the birth-and-death model of evolution. A comparison of sequence identity distributions between sets of homologous gene pairs shows that the different copies of tandem arrayed paralogs are less divergent than copies of dispersed paralogs in yeast genomes. It suggests that paralogs included in tandem structures are more recent or more subject to the gene conversion mechanism than other paralogs. Conclusion The method reported here is a useful computational tool to provide a database of TGAs composed of functional or nonfunctional gene copies. Such a database has obvious applications in the fields of structural and comparative genomics. Notably, a detailed study of the TGA catalog will make it possible to tackle the fundamental questions of the origin and evolution of tandem gene clusters.
Published: 2010
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