Descriptor: "MESH: Genome, Fungal" - Searchworks@Jio Institute Digital Library Search Results

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76 results on '"MESH: Genome, Fungal"'

1. A yeast living ancestor reveals the origin of genomic introgressions

Author: Karl Persson, Agnès Llored, Matteo De Chiara, Agurtzane Irizar, Simon Stenberg, Gianni Liti, Eric Gilson, Benjamin Barré, Jia-Xing Yue, Joseph Schacherer, Melania D’Angiolo, Jonas Warringer, Roberto Marangoni, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)
Subjects: [SDV]Life Sciences [q-bio], Lineage (evolution), Loss of Heterozygosity, yeast, Paradoxus, Genome, 0302 clinical medicine, MESH: Genetic Fitness, MESH: Genetic Introgression, Homologous Recombination, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, MESH: Reproduction, Asexual, 0303 health sciences, Multidisciplinary, biology, MESH: Genomic Instability, MESH: Genomics, Fungal genetics, Genomics, Reproductive isolation, MESH: Crosses, Genetic, MESH: Saccharomyces cerevisiae, Meiosis, yeast, Alpechin, genomic introgression, MESH: Genome, Fungal, Genome, Fungal, Mitosis, Alpechin, Introgression, Saccharomyces cerevisiae, Genetic Introgression, Genomic Instability, Evolution, Molecular, MESH: Homologous Recombination, Saccharomyces, 03 medical and health sciences, Reproduction, Asexual, Saccharomyces paradoxus, Crosses, Genetic, 030304 developmental biology, MESH: Loss of Heterozygosity, MESH: Saccharomyces, MESH: Fertility, genomic introgression, MESH: Mitosis, biology.organism_classification, MESH: Meiosis, Fertility, Evolutionary biology, Genetic Fitness, 030217 neurology & neurosurgery
Abstract: International audience; Genome introgressions drive evolution across the animal1, plant2 and fungal3 kingdoms. Introgressions initiate from archaic admixtures followed by repeated backcrossing to one parental species. However, how introgressions arise in reproductively isolated species, such as yeast4, has remained unclear. Here we identify a clonal descendant of the ancestral yeast hybrid that founded the extant Saccharomyces cerevisiae Alpechin lineage5, which carries abundant Saccharomyces paradoxus introgressions. We show that this clonal descendant, hereafter defined as a 'living ancestor', retained the ancestral genome structure of the first-generation hybrid with contiguous S. cerevisiae and S. paradoxus subgenomes. The ancestral first-generation hybrid underwent catastrophic genomic instability through more than a hundred mitotic recombination events, mainly manifesting as homozygous genome blocks generated by loss of heterozygosity. These homozygous sequence blocks rescue hybrid fertility by restoring meiotic recombination and are the direct origins of the introgressions present in the Alpechin lineage. We suggest a plausible route for introgression evolution through the reconstruction of extinct stages and propose that genome instability allows hybrids to overcome reproductive isolation and enables introgressions to emerge.
Published: 2020

2. La formation de néochromosomes au cours de l'évolution chez la levure Saccharomyces cerevisiae

Author: Agnès Thierry, Varun Khanna, Bernard Dujon, Génétique des génomes - Genetics of Genomes (UMR 3525), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This research was funded in part by contract DYGEVO from Agence Nationale pour la Recherche (France) under programme blanc 2011 section SVSE6., We thank Laurence Ma, Christiane Bouchier and all members of the genomic platform of Institut Pasteur for genomic sequences and our colleagues from the Unité de Génétique moléculaire des levures for fruitful discussions., and ANR-11-BSV6-0001,DYGEVO,Dynamique et évolution des génomes de levures, modèles eucaryotes unicellulaires.(2011)
Subjects: MESH: Repetitive Sequences, Nucleic Acid, Saccharomyces cerevisiae Proteins, Whole Genome Sequencing, palindrome, retrotransposon, Saccharomyces cerevisiae, QH426-470, yeast, amplification, MESH: Chromosomes, Fungal, MESH: Saccharomyces cerevisiae, Article, MESH: Saccharomyces cerevisiae Proteins, MESH: Directed Molecular Evolution, MESH: Genome, Fungal, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Chromosomes, Fungal, Directed Molecular Evolution, Genome, Fungal, MESH: Whole Genome Sequencing, genome, Repetitive Sequences, Nucleic Acid
Abstract: International audience; Novel, large-scale structural mutations were previously discovered during the cultivation of engineered Saccharomyces cerevisiae strains in which essential tRNA synthetase genes were replaced by their orthologs from the distantly related yeast Yarrowia lipolytica. Among those were internal segmental amplifications forming giant chromosomes as well as complex segmental rearrangements associated with massive amplifications at an unselected short locus. The formation of such novel structures, whose stability is high enough to propagate over multiple generations, involved short repeated sequences dispersed in the genome (as expected), but also novel junctions between unrelated sequences likely triggered by accidental template switching within replication forks. Using the same evolutionary protocol, we now describe yet another type of major structural mutation in the yeast genome, the formation of neochromosomes, with functional centromeres and telomeres, made of extra copies of very long chromosomal segments ligated together in novel arrangements. The novel junctions occurred between short repeated sequences dispersed in the genome. They first resulted in the formation of an instable neochromosome present in a single copy in the diploid cells, followed by its replacement by a shorter, partially palindromic neochromosome present in two copies, whose stability eventually increased the chromosome number of the diploid strains harboring it.
Published: 2021
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3. Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss

Author: Gröhs Ferrareze, Patrícia Aline, Maufrais, Corinne, Silva Araujo Streit, Rodrigo, Priest, Shelby, Cuomo, Christina, Heitman, Joseph, Staats, Charley Christian, Janbon, Guilhem, Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Duke University Medical Center, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], PAGF was supported by a CAPES exchange grant (Advanced Network of Computational Biology—RABICÓ – Grant no. 23038.010041/2013-13). This work was supported by a CAPES COFECUB grant n°39712ZK to GJ, by a CNPq grant (309897/2017-3) to CCS, and by a NIH/NIAID R37 MERIT Award AI39115-23 and a NIH/NIAID R01 Award AI50113-16 to JH. JH is co-director and fellow of CIFAR program Fungal Kingdom: Threats & Opportunities. SJP was supported by the NIH/NIAID F31 Fellowship 1F31AI143136-02., and Members of the Heitman laboratory are acknowledged for valuable discussion.
Subjects: AcademicSubjects/SCI01140, AcademicSubjects/SCI00010, genome annotation pipeline, MESH: Genomics, [SDV]Life Sciences [q-bio], MESH: RNA Interference, MESH: Cryptococcus neoformans, Molecular Sequence Annotation, MESH: Molecular Sequence Annotation, Genomics, Cryptococus deuterogattii, AcademicSubjects/SCI01180, metabolic gene cluster, RNAi, Multigene Family, MESH: Genome, Fungal, Fungal Genetics and Genomics, Cryptococcus neoformans, MESH: Multigene Family, AcademicSubjects/SCI00960, RNA Interference, Genome, Fungal
Abstract: International audience; Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary-based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results show that the quality of the annotation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5–10 million reads per RNA-seq replicate. We also showed that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient species C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and transporters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelomeric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.
Published: 2021

4. Computer vision for pattern detection in chromosome contact maps

Author: Axel Breuer, Axel Cournac, Antoine Vigouroux, Etienne Jean, Adrien Meot, Edgar Oriol, Romain Koszul, Laurent Politis, Arnaud Campeas, Nadège Guiglielmoni, Cyril Matthey-Doret, Lyam Baudry, Vittore F. Scolari, Philippe Henri Chanut, Pierrick Moreau, Rémi Montagne, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), ENGIE, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris], Département de Biologie Computationnelle - Department of Computational Biology, This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris. C.M.-D. was supported by the Pasteur—Paris University (PPU) International PhD Program. A.B. works within the framework of a 'Mécénat Compétence' contract of the company ENGIE. V.S. is the recipient of a Roux-Cantarini Pasteur fellowship. This research was supported by funding to R.K. from the European Research Council under the Horizon 2020 Program (ERC grant agreement 771813) and by ANR JCJC 2019, 'Apollo' allocated to A.C., This work was initiated during a Hackathon between Institut Pasteur scientists and ENGIE engineers. We would like to thank all the people that allow the organisation of this event especially Anne-Gaelle Coutris, Romain Tchertchian and Olivier Gascuel. Julien Mozziconacci, Frédéric Beckouët and all the members of Spatial Regulation of Genomes unit are thanked for stimulating discussions and feedback., ANR-19-CE45-0003,Apollo,Intelligence Artificielle pour atteindre la face cachée des chromosomes(2019), European Project: 771813,SynarchiC, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Institut Pasteur [Paris] (IP), and European Project: 771813,ERC-2017-COG,SynarchiC(2018)
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Genome informatics, Genome, Pattern Recognition, Automated, Workflow, Chromosome conformation capture, chemistry.chemical_compound, 0302 clinical medicine, Chromosomes, Human, MESH: Pattern Recognition, Automated, Computer vision, lcsh:Science, 0303 health sciences, Multidisciplinary, Fungal genetics, MESH: Chromosomes, Fungal, MESH: Saccharomyces cerevisiae, Chromatin, Data processing, Simulated data, MESH: Genome, Fungal, Pattern recognition (psychology), Chromosomes, Fungal, Genome, Fungal, Algorithms, MESH: Computers, Bioinformatics, Science, MESH: Algorithms, Saccharomyces cerevisiae, MESH: Chromosomes, Human, Chromosomes, Article, General Biochemistry, Genetics and Molecular Biology, MESH: Workflow, 03 medical and health sciences, Pattern detection, Code (cryptography), Humans, 030304 developmental biology, Nuclear organization, MESH: Humans, Computers, business.industry, Chromosome, General Chemistry, 030104 developmental biology, chemistry, lcsh:Q, MESH: Chromosomes, Artificial intelligence, business, DNA, 030217 neurology & neurosurgery
Abstract: Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols., Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Published: 2020

5. Use of CRISPR-Cas9 To Target Homologous Recombination Limits Transformation-Induced Genomic Changes in Candida albicans

Author: Christophe d'Enfert, Timea Marton, Corinne Maufrais, Mélanie Legrand, Biologie et Pathogénicité fongiques - Fungal Biology and Pathogenicity (BPF), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris Diderot, Sorbonne Paris Cité, Paris, France, Université Paris Diderot - Paris 7 (UPD7), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), T.M. is the recipient of a Ph.D. fellowship from the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID). We acknowledge support from the French Government’s Investissement d’Avenir program (Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases [ANR10-LABX-62-IBEID])., We are grateful to the members of the Institut Pasteur Mutualized Platform for Microbiology (P2M) for Illumina sequencing., and ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010)
Subjects: MESH: Gene Editing, MESH: CRISPR-Cas Systems, Molecular Biology and Physiology, [SDV]Life Sciences [q-bio], genome rearrangements, MESH: Transformation, Genetic, MESH: CRISPR-Associated Protein 9, Biology, Microbiology, Genome, Genome engineering, MESH: Homologous Recombination, 03 medical and health sciences, Transformation, Genetic, 0302 clinical medicine, Genome editing, MESH: RNA, Guide, CRISPR-Associated Protein 9, Candida albicans, CRISPR, Homologous Recombination, Molecular Biology, 030304 developmental biology, Gene Editing, Genetics, 0303 health sciences, MESH: Candida albicans, MESH: Genomics, Genomics, Editor's Pick, biology.organism_classification, QR1-502, Corpus albicans, Transformation (genetics), MESH: Genome, Fungal, CRISPR-Cas9, CRISPR-Cas Systems, Genome, Fungal, Homologous recombination, 030217 neurology & neurosurgery, Research Article, RNA, Guide, Kinetoplastida
Abstract: Genome editing is essential to nearly all research studies aimed at gaining insight into the molecular mechanisms underlying various biological processes, including those in the opportunistic pathogen Candida albicans. The adaptation of the CRISPR-Cas9 system greatly facilitates genome engineering in many organisms. However, our understanding of the effects of CRISPR-Cas9 technology on the biology of C. albicans is limited. In this study, we sought to compare the extents of transformation-induced genomic changes within strains engineered using CRISPR-Cas9-free and CRISPR-Cas9-dependent transformation methods. CRISPR-Cas9-dependent transformation allows one to simultaneously target both homologs and, importantly, appears less mutagenic in C. albicans, since strains engineered using CRISPR-Cas9 display an overall decrease in concomitant genomic changes., Most of our knowledge relating to molecular mechanisms of human fungal pathogenesis in Candida albicans relies on reverse genetics approaches, requiring strain engineering. DNA-mediated transformation of C. albicans has been described as highly mutagenic, potentially accentuated by the organism’s genome plasticity, including the acquisition of genomic rearrangements, notably upon exposure to stress. The advent of CRISPR-Cas9 has vastly accelerated the process of genetically modifying strains, especially in diploid (such as C. albicans) and polyploid organisms. The effects of unleashing this nuclease within the genome of C. albicans are unknown, although several studies in other organisms report Cas9-associated toxicity and off-target DNA breaks. Upon the construction of a C. albicans strain collection, we took the opportunity to compare strains which were constructed using CRISPR-Cas9-free and CRISPR-Cas9-dependent transformation strategies, by quantifying and describing transformation-induced loss-of-heterozygosity and hyperploidy events. Our analysis of 57 strains highlights the mutagenic effects of transformation in C. albicans, regardless of the transformation protocol, but also underscores interesting differences in terms of genomic changes between strains obtained using different transformation protocols. Indeed, although strains constructed using the CRISPR-Cas9-free transformation method display numerous concomitant genomic changes randomly distributed throughout their genomes, the use of CRISPR-Cas9 leads to a reduced overall number of genome changes, particularly hyperploidies. Overall, in addition to facilitating strain construction by reducing the number of transformation steps, the CRISPR-Cas9-dependent transformation strategy in C. albicans appears to limit transformation-associated genome changes. IMPORTANCE Genome editing is essential to nearly all research studies aimed at gaining insight into the molecular mechanisms underlying various biological processes, including those in the opportunistic pathogen Candida albicans. The adaptation of the CRISPR-Cas9 system greatly facilitates genome engineering in many organisms. However, our understanding of the effects of CRISPR-Cas9 technology on the biology of C. albicans is limited. In this study, we sought to compare the extents of transformation-induced genomic changes within strains engineered using CRISPR-Cas9-free and CRISPR-Cas9-dependent transformation methods. CRISPR-Cas9-dependent transformation allows one to simultaneously target both homologs and, importantly, appears less mutagenic in C. albicans, since strains engineered using CRISPR-Cas9 display an overall decrease in concomitant genomic changes.
Published: 2020

6. Population size, sex and purifying selection: comparative genomics of two sister taxa of the wild yeast Saccharomyces paradoxus

Author: José Paulo Sampaio, Gianni Liti, Vassiliki Koufopanou, Timothy A. Mousseau, Susan Lomas, Pedro Almeida, Olga Pronina, Austin Burt, Imperial College London, National Academy of Sciences of Ukraine (NASU), University College of London [London] (UCL), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), University of South Carolina [Columbia], Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Liti, Gianni, and Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: AcademicSubjects/SCI01140, 0106 biological sciences, Linkage disequilibrium, Lineage (evolution), MESH: Selection, Genetic, 0601 Biochemistry and Cell Biology, 01 natural sciences, Nucleotide diversity, Negative selection, MESH: Genetic Fitness, MESH: Genetic Variation, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Recombination, Genetic, 0303 health sciences, education.field_of_study, biology, Population size, latitude, MESH: Genome, Fungal, MESH: Recombination, Genetic, Genome, Fungal, Research Article, Population, generation time, 010603 evolutionary biology, diversity, Mutation Accumulation, Saccharomyces, 03 medical and health sciences, 0603 Evolutionary Biology, ρ, Genetics, Saccharomyces paradoxus, Selection, Genetic, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Mutation Accumulation, MESH: Saccharomyces, 0604 Genetics, Generation time, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], AcademicSubjects/SCI01130, Genetic Variation, biology.organism_classification, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, recombination, Evolutionary biology, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genetic Fitness, divergence, Developmental Biology
Abstract: This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.
Published: 2020

7. Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses

Author: Ana Belén Araúz, Elizabeth L. Berkow, Oliver Kurzai, Christopher H. Heath, Rodney Adam, Sahar Althawadi, Xiao Li, Shawn R. Lockhart, Patricia Escandón, Ronen Ben-Ami, Anastasia P. Litvintseva, Lalitha Gade, Alexandre Alanio, Revathi Gunturu, Kaitlin Forsberg, Ana Alastruey-Izquierdo, Nancy A. Chow, Christina A. Cuomo, Amrita Bharat, Marie Desnos-Ollivier, Dianne Gardam, Belinda Calvo, Ronny Martin, José F. Muñoz, Rory M. Welsh, Centers for Disease Control and Prevention (CDC), Broad Institute [Cambridge], Massachusetts Institute of Technology (MIT)-Harvard University [Cambridge], Aga Khan University Hospital (AKUH), Nairobi, Mycologie moléculaire - Molecular Mycology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris], Laboratoire de Parasitologie-Mycologie [CHU Saint Louis, Paris], Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Paris (UP), Instituto de Salud Carlos III [Madrid] (ISC), King Faisal Specialist Hospital and Research Centre, Riyadh, Hospital Santo Tomás, Tel Aviv Sourasky Medical Center [Te Aviv], Tel Aviv University [Tel Aviv], Public Health Agency of Canada (PHAC), Universidad del Zulia (LUZ), Instituto Nacional de Salud [Bogota], Fiona Stanley Hospital [Murdoch], Royal Perth Hospital, The University of Western Australia (UWA), Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), University of Würzburg = Universität Würzburg, This project has been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under award U19AI110818 to the Broad Institute. C.A.C. is a CIFAR fellow in the Fungal Kingdom Program. This work was also made possible through support from the Advanced Molecular Detection (AMD) initiative at CDC., National Institute of Allergy and Infectious Diseases (United States), Harvard University-Massachusetts Institute of Technology (MIT), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Université Paris Cité (UPCité), King Faisal Specialist Hospital and Research Centre (KFSH & RC), and Tel Aviv University (TAU)
Subjects: Azoles, Antifungal Agents, Population genetics, Emerging species, Echinocandins, MESH: Azoles, Molecular clock, Clade, MESH: Phylogeny, Fluconazole, Phylogeny, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Candida, genome analysis, emerging species, 0303 health sciences, education.field_of_study, Molecular Epidemiology, Candida auris, antifungal resistance, Biological Evolution, QR1-502, 3. Good health, Phylogeography, MESH: Phylogeography, MESH: Genome, Fungal, MESH: Fluconazole, Genome, Fungal, MESH: Metagenomics, MESH: Whole Genome Sequencing, Research Article, MESH: Mutation, Population, Genes, Fungal, MESH: Genetics, Population, Context (language use), MESH: Biological Evolution, Ecological and Evolutionary Science, Biology, Microbiology, MESH: Drug Resistance, Fungal, 03 medical and health sciences, Phylogenetics, Drug Resistance, Fungal, MESH: Candida, Virology, Humans, MESH: Molecular Epidemiology, Candidiasis, Invasive, education, 030304 developmental biology, MESH: Humans, Molecular epidemiology, Whole Genome Sequencing, 030306 microbiology, MESH: Echinocandins, population genetics, Antifungal resistance, Genome analysis, MESH: Antifungal Agents, MESH: Candidiasis, Invasive, Genetics, Population, Evolutionary biology, Mutation, Metagenomics, MESH: Genes, Fungal
Abstract: In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology., Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.
Published: 2020

8. Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom

Author: Frédérique Moyrand, Prashanthi Natarajan, Guilhem Janbon, Jade Sales-Lee, Laura R. Tuck, Frank Feuerbach, Wallace Ewj, Luciana de Oliveira, Hiten D. Madhani, Corinne Maufrais, Centre for Synthetic and Systems Biology (Ssynthsys), University of Edinburgh, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP), Department of Biochemistry and Biophysics [San Francisco], University of California (UC), Génétique des Interactions macromoléculaires / Genetics of Macromolecular Interactions, Chan Zuckerberg BioHub [San Francisco, CA], This work in the Madhani lab was supported by grants from the US National Institutes of Health [R01AI120464, R01GM71801 to H.D.M.], H.D.M. is an Investigator of the Chan-Zuckerberg Biohub, E.W.J.W. is a Sir Henry Dale Fellow, supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society [208779/Z/17/Z], L.T. is supported by a Wellcome-University of Edinburgh ISSF3 award, This work in the Janbon lab was supported by an Infect-ERA grant (project Cryptoview). Funding for open access charge: University of Edinburgh., We thank members of the Wallace, Janbon, and Madhani labs for helpful discussions and comments on the manuscript. We thank Juan Mata for sharing intermediate data related to (59). We are grateful to J. Weissman (UCSF) for advice on ribosome profiling. We thank three anonymous reviewers for their helpful comments., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], University of California, and Génétique des Interactions macromoléculaires
Subjects: Kozak consensus sequence, Codon, Initiator, MESH: Gene Expression Regulation, Fungal, MESH: Saccharomyces cerevisiae / metabolism, Ribosome, 0302 clinical medicine, Start codon, Gene Expression Regulation, Fungal, MESH: Neurospora crassa / metabolism, Candida albicans, MESH: Schizosaccharomyces / metabolism, Peptide Chain Initiation, Translational, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, 0303 health sciences, Chromosome Mapping, Translation (biology), MESH: Codon, Initiator / chemistry, MESH: Candida albicans / genetics, Transfer RNA, Genome, Fungal, MESH: Genome, Fungal, MESH: Codon, Initiator / metabolism, MESH: Peptide Chain Initiation, Translational, Context (language use), Saccharomyces cerevisiae, Data Resources and Analyses, MESH: Amino Acyl-tRNA Synthetases / genetics, Biology, Amino Acyl-tRNA Synthetases, Open Reading Frames, 03 medical and health sciences, Species Specificity, Schizosaccharomyces, MESH: Neurospora crassa / genetics, MESH: Species Specificity, Gene, MESH: Cryptococcus / metabolism, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Neurospora crassa, MESH: Schizosaccharomyces / genetics, MESH: Cryptococcus / genetics, MESH: Open Reading Frames, MESH: Saccharomyces cerevisiae / genetics, Cryptococcus, Open reading frame, MESH: Amino Acyl-tRNA Synthetases / metabolism, MESH: Chromosome Mapping, MESH: Candida albicans / metabolism, 030217 neurology & neurosurgery
Abstract: Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5′ and 3′ ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
Published: 2020

9. Developing a tetO/TetR system in Neurospora crassa

Author: Eugene Gladyshev, Tinh-Suong Nguyen, Epigénomique fongique - Fungal Epigenomics, Institut Pasteur [Paris] (IP), The work was supported by grants from the Agence Nationale de la Recherche (10-LABX-0062) and Fondation pour la Recherche Médicale (AJE20180539525)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Institut Pasteur [Paris]
Subjects: Photomicrography, TetR, Operator Regions, Genetic, MESH: Genes, Synthetic, FROS, MESH: Neurospora crassa, MESH: Tetracycline, Green fluorescent protein, chemistry.chemical_compound, Gene Expression Regulation, Fungal, Genes, Synthetic, Fluorescence microscope, Homologous Recombination, 0303 health sciences, biology, Cell biology, DNA-Binding Proteins, MESH: Repressor Proteins, MESH: Genome, Fungal, MESH: Fungal Proteins, Genome, Fungal, Fluorescent repressor operator system, MESH: Gene Expression Regulation, Fungal, MESH: Photomicrography, Recombinant Fusion Proteins, Genes, Fungal, Microbiology, Neurospora, Neurospora crassa, Fungal Proteins, MESH: Homologous Recombination, 03 medical and health sciences, Genetics, Homologous chromosome, MESH: Recombinant Fusion Proteins, Point Mutation, Gene, tetO, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, MESH: Point Mutation, MESH: Repetitive Sequences, Nucleic Acid, 030306 microbiology, Point mutation, fungi, MESH: Saporins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Tetracycline, biology.organism_classification, Saporins, Repressor Proteins, chemistry, RIP, MESH: Operator Regions, Genetic, Repeat-induced point mutation, MESH: Genes, Fungal, MESH: DNA-Binding Proteins
Abstract: International audience; The development of a tetO/TetR system in the fungus Neurospora crassa is described. The system includes (i) a synthetic gene encoding a TetR variant fused to GFP, and (ii) a standard tetO array integrated homologously, as a proof of principle, near the his-3 gene. The localization of TetR-GFP at the tetO array (observed by fluorescence microscopy) can be disrupted by the application of tetracycline. The full-length array is stable during vegetative growth, but it triggers strong repeat-induced point mutation (RIP) by the RID-dependent as well as the DIM-2-dependent pathways during the sexual phase. Thus, both RIP pathways must be inactivated to allow the faithful inheritance of the unmodified construct. In summary, this study introduces a new molecular tool into Neurospora research, and suggests that the standard tetO array can self-engage in recombination-independent homologous pairing.
Published: 2020

10. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites

Author: Isabelle P. Oswald, Emilien L. Jamin, Thaïs Hautbergue, Olivier Puel, Laurent Debrauwer, ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, MetaboHUB, Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), This study was co-funded by INRA and French Minister of Higher Education and Research in the context of a project supported by French National Agency of Research (ANR-15-CE21-0010-21Newmyco), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-MetaToul-MetaboHUB, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-15-CE21-0010,Newmyco,Metabolome de deux contaminants fongiques du blé d'importance majeure: identification de nouveaux métabolites toxiques(2015), ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-MetaboHUB-MetaToul, Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), OSWALD, Isabelle, Metabolome de deux contaminants fongiques du blé d'importance majeure: identification de nouveaux métabolites toxiques - - Newmyco2015 - ANR-15-CE21-0010 - AAPG2015 - VALID, and Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation - - METABOHUB2011 - ANR-11-INBS-0010 - INBS - VALID
Subjects: Proteomics, 0301 basic medicine, MESH: Isotope Labeling, MESH: Genomics / methods, [SDV]Life Sciences [q-bio], Secondary Metabolism, Biochemistry, Gene Knockout Techniques, Drug Discovery, Data Mining, MESH: Gene Knockout Techniques, Animal health, Drug discovery, Culture environment, Genomics, MESH: Proteomics / methods, [SDV.TOX] Life Sciences [q-bio]/Toxicology, MESH: Secondary Metabolism, [SDV.TOX.TVM] Life Sciences [q-bio]/Toxicology/Vegetal toxicology and mycotoxicology, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Isotope Labeling, Multigene Family, MESH: Genome, Fungal, Identification (biology), Genome, Fungal, MESH: Metabolomics / methods, Emerging technologies, [SDV.TOX.TVM]Life Sciences [q-bio]/Toxicology/Vegetal toxicology and mycotoxicology, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, Computational biology, Biology, 03 medical and health sciences, Metabolomics, MESH: Computer Simulation, MESH: Drug Discovery, Computer Simulation, MESH: Biological Products / metabolism, Secondary metabolism, MESH: Biological Products / isolation & purification, Biological Products, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, MESH: Fungi / metabolism, Organic Chemistry, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Fungi, MESH: Fungi / genetics, MESH: Data Mining / methods, 030104 developmental biology, [SDV.TOX.TCA] Life Sciences [q-bio]/Toxicology/Toxicology and food chain, MESH: Multigene Family
Abstract: International audience; Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
Published: 2018

11. Introns in Cryptococcus

Author: Guilhem Janbon, Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris], Acknowledgements to Cecelia Shertz Wall for editing the manuscript., and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Microbiology (medical), Transposable element, MESH: Sequence Analysis, DNA, lcsh:Arctic medicine. Tropical medicine, intron, lcsh:RC955-962, 030106 microbiology, lcsh:QR1-502, Cryptococcus, Review, yeast, lcsh:Microbiology, 03 medical and health sciences, alternative splicing, DNA, Fungal, Gene, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Cryptococcus neoformans, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Alternative splicing, Intron, RNA, MESH: Cryptococcus / genetics, Sequence Analysis, DNA, Genome project, biology.organism_classification, Introns, MESH: DNA, Fungal, 030104 developmental biology, MESH: Introns / genetics, MESH: Genome, Fungal, Genome, Fungal
Abstract: International audience; In Cryptococcus neoformans, nearly all genes are interrupted by small introns. In recent years, genome annotation and genetic analysis have illuminated the major roles these introns play in the biology of this pathogenic yeast. Introns are necessary for gene expression and alternative splicing can regulate gene expression in response to environmental cues. In addition, recent studies have revealed that C. neoformans introns help to prevent transposon dissemination and protect genome integrity. These characteristics of cryptococcal introns are probably not unique to Cryptococcus, and this yeast likely can be considered as a model for intron-related studies in fungi.
Published: 2018

12. Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

Author: Eva H. Stukenbrock, Julien Y. Dutheil, Max Planck Institute for Evolutionary Biology, Max-Planck-Gesellschaft, Christian-Albrechts University of Kiel, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Recombination hotspot, 01 natural sciences, Genome, Linkage Disequilibrium, Nucleotide diversity, Population genomics, MESH: Plant Diseases, Zymoseptoria, Crossing Over, Genetic, Population and Evolutionary Genetics, MESH: Evolution, Molecular, Genetics, Recombination, Genetic, recombination analyses, Base Composition, MESH: Polymorphism, Single Nucleotide, MESH: Genomics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, Chromosome Mapping, Genomics, MESH: Chromosomes, Fungal, MESH: Linkage Disequilibrium, MESH: Genome, Fungal, recombination hotspots, MESH: Recombination, Genetic, MESH: Centromere, Chromosomes, Fungal, Genome, Fungal, Recombination, effectors, Genome evolution, Centromere, fungal plant pathogens, MESH: Ascomycota, Biology, Investigations, genome evolution, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, MESH: Base Composition, Ascomycota, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Crossing Over, Genetic, Plant Diseases, [SDV.GEN]Life Sciences [q-bio]/Genetics, 030104 developmental biology, Homologous recombination, MESH: Chromosome Mapping, 010606 plant biology & botany
Abstract: Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species.
Published: 2017

13. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Author: Du, C, Gryganskyi, G, Tschaplinski, R, Misztal, C, Wu, A, Desirò, I, Vande Pol, I, Du, R, Zienkiewicz, R, Zienkiewicz, G, Tisserant, R, Splivallo, G, Hainaut, R, Henrissat, R, Ohm, R., Kuo, G, Yan, G., Lipzen, G, Nolan, G, LaButti, G, Barry, G, Goldstein, G, Labbe, R., Schadt, R, Tuskan, G., Grigoriev, G, Martin, R, Vilgalys, R., Bonito, G., Du, J., Gryganskyi, A., Du, K., Tschaplinski, T., Misztal, K., Wu, S., Desirò, A., Vande Pol, N., Du, Z., Zienkiewicz, A., Zienkiewicz, K., Morin, E., Tisserant, E., Splivallo, R., Hainaut, M., Henrissat, B., Kuo, A., Yan, J., Lipzen, A., Nolan, M., LaButti, K., Barry, K., Goldstein, A., Labbé, J., Schadt, C., Grigoriev, I., Martin, F., Duke University [Durham], BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, University of California [Berkeley], University of California, Arizona State University [Tempe] (ASU), Deparment of Plant, Soil and Microbial Sciences, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Goethe-University Frankfurt am Main, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Utrecht University [Utrecht], Genomic Science Program, U.S. Department of Energy, Office of Science - Biological and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area at Oak Ridge National Laboratory, U.S. Department of Energy DE-AC05- 00OR22725, DOE Joint Genome Institute by the JGI Community sequencing program 570, Office of Science of the US Department of Energy DE-AC02-05CH11231, EU Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE) ANR-11-LABX-0002-01, Joint Genome Institute (JGI), Northwest Institute for Nonferrous Metal Research (NIN), Laboratorio de Turbulencia, Universidad de Santiago de Chile [Santiago] (USACH), UT-Battelle, LLC, Centre d'études de chimie métallurgique (CECM), Centre National de la Recherche Scientifique (CNRS), Kansas State University, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Center for Human Genetics, University of Leuven School of Medicine, SCHOOL of MEDICINE [Louvain], Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Sub Molecular Microbiology, Molecular Microbiology, Joint Genome Institute ( JGI ), Northwest Institute for Nonferrous Metal Research, Oak Ridge National Laboratory, Duke university [Durham], Centre d'études de chimie métallurgique ( CECM ), Centre National de la Recherche Scientifique ( CNRS ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), UNIVERSITY of LEUVEN SCHOOL of MEDICINE, Institute of Northern Engineering, 455 Duckering Bldg, Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), University of California [Berkeley] (UC Berkeley), and University of California (UC)
Subjects: Burkholderiaceae, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH : Symbiosis, MESH: Base Sequence, MESH: Genome, Bacterial, 2.2 Factors relating to physical environment, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, LAND PLANTS, 2.2 Factors relating to the physical environment, MESH : Metagenome, MESH: Animals, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, Phylogeny, MESH: Lipid Metabolism, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Symbiosis, Endosymbiosis, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Bacterial, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], FATTY-ACID BIOSYNTHESIS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Fungal, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Infection, Evolution, 030106 microbiology, MESH : Genome, Bacterial, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, GENE-TRANSFER, 03 medical and health sciences, MESH : Burkholderiaceae, Botany, MESH : Evolution, Molecular, Ecology, Evolution, Behavior and Systematics, Comparative genomics, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, MESH : Genome, Fungal, Molecular, ENDOBACTERIA, MESH: Burkholderiaceae, DNA, 15. Life on land, Lipid Metabolism, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, INTRACELLULAR BACTERIA, 030104 developmental biology, MESH: Mortierella, Metagenome, MESH : Sequence Analysis, DNA, 0301 basic medicine, MESH: Sequence Analysis, DNA, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH: Carbohydrate Metabolism, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome, GUT MICROBIOME, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, ARBUSCULAR MYCORRHIZAL FUNGI, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Mortierella, MESH : Lipid Metabolism, MESH: Evolution, Molecular, 2. Zero hunger, Genetics, biology, Ecology, Fungal genetics, MESH : Carbohydrate Metabolism, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], ESCHERICHIA-COLI, Carbohydrate Metabolism, Sequence Analysis, Metabolic Networks and Pathways, CANDIDATUS GLOMERIBACTER GIGASPORARUM, Bacterial genome size, Symbiosis, Behavior and Systematics, Lipid biosynthesis, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Evolutionary Biology, Base Sequence, MESH : Metabolic Networks and Pathways, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH: Metagenome, biology.organism_classification, MESH: Metabolic Networks and Pathways, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH : Base Sequence, BICOLOR S238N, MESH : Animals, MESH : Mortierella, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.
Published: 2017

14. Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels

Author: Igor V. Grigoriev, Weihua Wu, John M. Gladden, Sirma Mihaltcheva, Kerrie Barry, Bernard Henrissat, Mary Bao Tran-Gyamfi, Mansi Chovatia, Alan Kuo, Erika Lindquist, Hope Hundley, Ryan W. Davis, Kurt LaButti, US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Dept Energy Great Lakes Bioenergy Res Ctr, University of California, Joint Genome Institute, United States Department of Energy, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), University of California (UC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), U.S. Department of Energy ( DOE ) -U.S. Department of Energy ( DOE ), Architecture et fonction des macromolécules biologiques ( AFMB ), and Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA )
Subjects: Ligninolytic enzymes, MESH : Polysaccharides, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Lignin, 7. Clean energy, Terpene, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH : Volatile Organic Compounds, Endophytes, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, Phylogeny, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], General Medicine, MESH : Glycoside Hydrolases, Volatile organic compound, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, CAZy, MESH: Sesquiterpenes, MESH: Fungal Proteins, Genome, Fungal, MESH: Monoterpenes, Sesquiterpenes, MESH: Gene Expression, Glycoside Hydrolases, 030106 microbiology, MESH: Alkyl and Aryl Transferases, MESH : Biofuels, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 03 medical and health sciences, Botany, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, Alkyl and Aryl Transferases, MESH : Genome, Fungal, MESH: Cellulase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH : Gene Expression, MESH : Monoterpenes, 030104 developmental biology, chemistry, Biofuels, MESH : Cellulases, 0301 basic medicine, MESH: Xylariales, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH : Endophytes, MESH: Cellulases, Gene Expression, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Applied Microbiology and Biotechnology, Endophyte, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, chemistry.chemical_compound, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Cellulases, MESH : Fungal Proteins, 2. Zero hunger, Xylariales, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biofuel, Biotechnology, MESH : Sesquiterpenes, Cellulase, Biology, Plant use of endophytic fungi in defense, MESH: Endophytes, MESH: Volatile Organic Compounds, Fungal Proteins, Consolidated bioprocessing, Polysaccharides, MESH : Xylariales, MESH: Glycoside Hydrolases, Bioprocess, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH : Alkyl and Aryl Transferases, MESH: Biofuels, Volatile Organic Compounds, MESH : Lignin, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, biology.organism_classification, MESH: Lignin, MESH: Polysaccharides, MESH : Cellulase, Monoterpenes, biology.protein, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and β-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms.
Published: 2017

15. Intron retention-dependent gene regulation in Cryptococcus neoformans

Author: Estelle Mogensen, Guilhem Janbon, Jungwook Hwang, Rony Barboux, Chung-Chau Hon, Pierre Lechat, Sara Gonzalez-Hilarion, Giovanni Bussotti, Kyung-Tae Lee, Damien Paulet, Jean Yves Coppée, Yong Sun Bahn, Caroline Proux, Frédérique Moyrand, Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris], Transcriptome et Epigénome (PF2), College of Life and Biotechnology [Séoul], Yonsei University, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Hanyang University, This work was supported by National Research Foundation of Korea grants (2015R1A2A1A15055687) from MEST, the Strategic Initiative for Microbiomes in Agriculture and Food funded by Ministry of Agriculture, Food and Rural Affairs (916006-2) (to Y.S.B). This work was supported by a grant from ANR (2010-BLAN-1620-01 program YeastIntrons) to GJ. We thank Tae-Yup Kim and Anna Floyd for their technical assistance. We thank Cecelia Shertz Wall for editing the manuscript., ANR-10-BLAN-1620,YeastIntrons,Analyse globale de la régulation des ARN contenant des PTC par la voie du NMD et le complexe EJC-like chez des levures riches ou pauvres en introns(2010), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, MESH: Proteome / metabolism, MESH: Gene Expression, Proteome, RNA Stability, 030106 microbiology, MESH: Proteome / genetics, Gene Expression, MESH: Gene Expression Regulation, Fungal, MESH: Molecular Sequence Annotation, Article, Fungal Proteins, 03 medical and health sciences, MESH: Introns, Fungal genetics, Gene Expression Regulation, Fungal, Gene expression, MESH: Fungal Proteins / genetics, Gene, MESH: Cryptococcus neoformans / genetics, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Cryptococcus neoformans, Genetics, Regulation of gene expression, Fungal protein, Multidisciplinary, biology, MESH: Alternative Splicing, Alternative splicing, Intron, MESH: RNA Stability, Molecular Sequence Annotation, biology.organism_classification, Introns, Alternative Splicing, 030104 developmental biology, MESH: Genome, Fungal, MESH: Cryptococcus neoformans / metabolism, MESH: Fungal Proteins / metabolism, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Fungal
Abstract: The biological impact of alternative splicing is poorly understood in fungi, although recent studies have shown that these microorganisms are usually intron-rich. In this study, we re-annotated the genome of C. neoformans var. neoformans using RNA-Seq data. Comparison with C. neoformans var. grubii revealed that more than 99% of ORF-introns are in the same exact position in the two varieties whereas UTR-introns are much less evolutionary conserved. We also confirmed that alternative splicing is very common in C. neoformans, affecting nearly all expressed genes. We also observed specific regulation of alternative splicing by environmental cues in this yeast. However, alternative splicing does not appear to be an efficient method to diversify the C. neoformans proteome. Instead, our data suggest the existence of an intron retention-dependent mechanism of gene expression regulation that is not dependent on NMD. This regulatory process represents an additional layer of gene expression regulation in fungi and provides a mechanism to tune gene expression levels in response to any environmental modification.
Published: 2016

16. A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi

Author: Jan Schirawski, Julien Y. Dutheil, Martin Münsterkötter, Gertrud Mannhaupt, Regine Kahmann, Gabriel Schweizer, Ulrich Güldener, Christian M. K. Sieber, Department of Organismic Interactions [Marburg], Max Planck Institute for Terrestrial Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Ustilago, 01 natural sciences, Genome, gene cluster, MESH: Saccharum, MESH: Plant Diseases, Gene cluster, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, biology, MESH: Genomics, MESH: Gene Duplication, Genomics, Saccharum, MESH: DNA Transposable Elements, Multigene Family, MESH: Genome, Fungal, MESH: Fungal Proteins, Genome, Fungal, Research Article, Transposable element, Genome evolution, repeat sequences, effector proteins, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, Phylogenetics, ddc:570, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene, Ecology, Evolution, Behavior and Systematics, selection interference, Effector Proteins, Gene Cluster, Gene Duplication, Genome Architecture, Repeat Sequences, Selection Interference, Plant Diseases, genome architecture, gene duplication, biology.organism_classification, 030104 developmental biology, DNA Transposable Elements, MESH: Multigene Family, MESH: Ustilago, 010606 plant biology & botany
Abstract: Genome biology and evolution 8(3), 681 - 704 (2016). doi:10.1093/gbe/evw026, Published by Oxford Univ. Press, Oxford
Published: 2016
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17. The 2008 update of the Aspergillus nidulans genome annotation: A community effort

Author: Wortman, Jennifer Russo, Gilsenan, Jane Mabey, Joardar, Vinita, Deegan, Jennifer, Clutterbuck, John, Andersen, Mikael R., Archer, David, Bencina, Mojca, Braus, Gerhard, Coutinho, Pedro, von Doehren, Hans, Doonan, John, Driessen, Arnold J. M., Durek, Pawel, Espeso, Eduardo, Fekete, Erzsebet, Flipphi, Michel, Garcia Estrada, Carlos, Geysens, Steven, Goldman, Gustavo, de Groot, Piet W. J., Hansen, Kim, Harris, Steven D., Heinekamp, Thorsten, Helmstaedt, Kerstin, Henrissat, Bernard, Hofmann, Gerald, Homan, Tim, Horio, Tetsuya, Horiuchi, Hiroyuki, James, Steve, Jones, Meriel, Karaffa, Levente, Karanyi, Zsolt, Kato, Masashi, Keller, Nancy, Kelly, Diane E., Kiel, Jan A. K. W., Kim, Jung-Mi, van der Klei, Ida J., Klis, Frans M., Kovalchuk, Andriy, Krasevec, Nada, Kubicek, Christian P., Liu, Bo, MacCabe, Andrew, Meyer, Vera, Mirabito, Pete, Miskei, Marton, Mos, Magdalena, Mullins, Jonathan, Nelson, David R., Nielsen, Jens, Oakley, Berl R., Osmani, Stephen A., Pakula, Tiina, Paszewski, Andrzej, Paulsen, Ian, Pilsyk, Sebastian, Pocsi, Istvan, Punt, Peter J., Ram, Arthur F. J., Ren, Qinghu, Robellet, Xavier, Robson, Geoff, Seiboth, Bernhard, van Solingen, Piet, Specht, Thomas, Sun, Jibin, Taheri-Talesh, Naimeh, Takeshita, Norio, Ussery, Dave, Vankuyk, Patricia A., Visser, Hans, de Vondervoort, Peter J. I. van, Walton, Jonathan, Xiang, Xin, Xiong, Yi, Zeng, An Ping, Brandt, Bernd W., Cornell, Michael J., van den Hondel, Cees A. M. J. J., Visser, Jacob, Oliver, Stephen G., Turner, Geoffrey, Kraševec, Nada, Kuyk, Patricia A. van, Döhren, D.H., van Seilboth, B, de Vries, R., Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Instituto de Agroquimica y Tecnologia de Alimentos (IATA), Instituto de Agroquímica y Tecnología de Alimentos - Institute of Agrochemistry and Food Technology [Valencia] (IATA-CSIC), Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, Molecular Cell Biology, Faculty of Science and Engineering, Host-Microbe Interactions, Man, Biomaterials and Microbes (MBM), Centre for World Food Studies, Bioinformatics, Bio Informatics (IBIVU), Integrative Bioinformatics, Molecular Biology and Microbial Food Safety (SILS, FNWI), and Mass Spectrometry of Biomacromolecules (SILS, FNWI)
Subjects: GENE-CLUSTER, PREDICTION, Assembly, Biológiai tudományok, CADRE, Genome, Természettudományok, CELL-WALL, Genetics, 0303 health sciences, Fungal protein, biology, MESH: Aspergillus nidulans, MESH: Genomics, Fungal community, Genomics, Genome project, Fungal, Aspergillus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Genome, Fungal, Identification (biology), MESH: Fungal Proteins, Genome, Fungal, fungal community, Annotation, Genes, Fungal, Computational biology, Vertebrate and Genome Annotation Project, SEQUENCE, Microbiology, Article, Aspergillus nidulans, Fungal Proteins, 03 medical and health sciences, transcription factors, Transcription factors, BIOSYNTHESIS, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, A-FUMIGATUS, genome, 030304 developmental biology, IDENTIFICATION, 030306 microbiology, DNA, NIGER, biology.organism_classification, TRANSCRIPTIONAL ACTIVATOR, Genes, Aspergilli, MESH: Genes, Fungal
Abstract: 12 páginas, 2 tablas -- PAGS nros. S2-S13, et al, The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology, We acknowledge financial support by the European Commission under contract LSSG-CT-2005-018964
Published: 2009

18. S. pombe LSD1 Homologs Regulate Heterochromatin Propagation and Euchromatic Gene Transcription

Author: Robert A. Martienssen, Fei Lan, Danesh Moazed, Yujiang Shi, Yang Shi, Maite Huarte, Steven P. Gygi, Matthew W. Vaughn, Judit Villén, André Verdel, Mikel Zaratiegui, Department of pathology, Harvard Medical School [Boston] (HMS), Cold Spring Harbor Laboratory (CSHL), Department of cell biology, and Verdel, Andre
Subjects: Transcription, Genetic, Euchromatin, MESH: Sequence Homology, Amino Acid, Cell Survival, Heterochromatin, MESH: Oxidoreductases, N-Demethylating, Molecular Sequence Data, MESH: Amino Acid Sequence, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, Histones, MESH: DNA Methylation, Gene Expression Regulation, Fungal, Schizosaccharomyces, Demethylase activity, Amino Acid Sequence, Epigenetics, Molecular Biology, MESH: Histones, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, MESH: Transcription, Genetic, EZH2, MESH: Schizosaccharomyces pombe Proteins, Oxidoreductases, N-Demethylating, Promoter, Cell Biology, DNA Methylation, MESH: Schizosaccharomyces, MESH: Heterochromatin, Histone, MESH: Cell Survival, MESH: Euchromatin, MESH: Genome, Fungal, biology.protein, Heterochromatin protein 1, Schizosaccharomyces pombe Proteins, Genome, Fungal, MESH: Gene Expression Regulation, Fungal
Abstract: International audience; LSD1 represses and activates transcription by demethylating histone H3K4me and H3K9me, respectively. Genetic ablation of the S. pombe homologs, splsd1 and splsd2, resulted in slow growth and lethality, respectively, underscoring their physiological importance. spLsd1 and spLsd2 form a stable protein complex, which exhibits demethylase activity toward methylated H3K9 in vitro. Both proteins were associated with the heterochromatin boundary regions and euchromatic gene promoters. Loss of spLsd1 resulted in increased H3K9 methylation accompanied by reduced euchromatic gene transcription and heterochromatin propagation. Removal of the H3K9 methylase Clr4 partially suppressed the slow growth phenotype of splsd1Delta. Conversely, catalytically inactivating point mutations in the splsd1 and splsd2 genes partially mimicked the growth and heterochromatin propagation phenotypes. Taken together, these findings suggest the importance of both enzymatic and nonenzymatic roles of spLsd1 in regulating heterochromatin propagation and euchromatic transcription and also suggest that misregulation of spLsd1/2 is likely to impact the epigenetic state of the cell.
Published: 2007
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19. The potential of whole genome NGS for infectious disease diagnosis

Author: Marc Eloit, Marc Lecuit, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service des Maladies infectieuses et tropicales [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Découverte de Pathogènes - Pathogen Discovery, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), M Eloit is the founder and CSO of Pathoquest (Paris, France), a spin out of Institut Pasteur dedicated to diagnostic of infectious diseases by NGS. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed., Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP]-Institut des Maladies Génétiques Imagine [Paris]
Subjects: Standardization, [SDV]Life Sciences [q-bio], diagnostic, Computational biology, Genome, Viral, virus, Biology, Bioinformatics, infectious diseases, MESH: Genome, Bacterial, Genome, Communicable Diseases, Deep sequencing, Pathology and Forensic Medicine, Standard procedure, Infectious disease diagnosis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, Humans, In patient, bacteria, Molecular Biology, MESH: Genome, Microbial, MESH: High-Throughput Nucleotide Sequencing, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, fungus, High-Throughput Nucleotide Sequencing, 3. Good health, Genome, Microbial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, NGS, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Communicable Diseases, Molecular Medicine, Identification (biology), Genome, Fungal, MESH: Genome, Viral, Genome, Bacterial, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Erratum in Corrigendum. [Expert Rev Mol Diagn. 2016]; International audience; Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.
Published: 2015

20. Generation and Analysis of Chromosomal Contact Maps of Yeast Species

Author: Cournac, Axel, Marbouty, Martial, Mozziconacci, Julien, Koszul, Romain, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), This research was supported by funding to R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013) / ERC grant agreement 260822. M.M. is the recipient of an Association pour la Recherche sur le Cancer fellowship 20100600373, European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Physique Théorique de la Matière Condensée ( LPTMC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), and European Project : 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG ( 2011 )
Subjects: Chromosome conformation capture, Genome assembly, MESH : Chromatin, [ SDV ] Life Sciences [q-bio], MESH : Chromosomes, Fungal, MESH : Genome, Fungal, [SDV]Life Sciences [q-bio], MESH : Saccharomyces cerevisiae, Chromosome Mapping, Saccharomyces cerevisiae, Genome organization, MESH: Chromosomes, Fungal, MESH: Saccharomyces cerevisiae, Yeast, Chromatin, MESH: Chromatin, MESH: Genome, Fungal, Chromosomes, Fungal, Genome, Fungal, 3C, MESH: Chromosome Mapping, MESH : Chromosome Mapping, 3C analysis
Abstract: International audience; Genome-wide derivatives of the chromosome conformation capture (3C) technique are now well-established approaches to study the multiscale average organization of chromosomes from bacteria to mammals. However, the experimental parameters of the protocol have to be optimized for different species, and the downstream experimental products (i.e., pair-end sequences) are influenced by these parameters. Here, we describe a complete pipeline to generate 3C-seq libraries and compute chromosomal contact maps of yeast species.
Published: 2015

21. Genome-wide replication landscape of Candida glabrata

Author: Cyril Saguez, Christiane Bouchier, Romain Koszul, Stéphane Descorps-Declère, Guy-Franck Richard, Laurence Ma, Martial Marbouty, Thomas Rolland, Bernard Dujon, Axel Cournac, Ivan Moszer, Centre d'Informatique pour la Biologie, Institut Pasteur [Paris], Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Génomique (Plate-Forme) - Genomics Platform, Institut de neurosciences translationnelles de Paris (NeurATRIS - IHU-A-ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Pasteur [Paris] (IP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC) - Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), CNRS UMR3225, Régulation spatiale des Génomes, Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Génétique humaine et Fonctions cognitives, Plateforme génomique, Université Pierre et Marie Curie - Paris 6 (UPMC) - CHU Pitié-Salpêtrière [APHP], Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA Replication, Physiology, Autonomously replicating sequence, [SDV]Life Sciences [q-bio], Genes, Fungal, Replication, MESH: Cell Cycle, MESH: DNA Replication, Candida glabrata, Plant Science, Biology, Origin of replication, Genome, General Biochemistry, Genetics and Molecular Biology, Chromosome conformation capture, Control of chromosome duplication, Tandem repeat, Structural Biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Candida glabrata, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Genetics, Megasatellites, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Cell Cycle, DNA replication, Cell Biology, biology.organism_classification, ACS, MESH: Chromosomes, Fungal, Yeast, [SDV] Life Sciences [q-bio], MESH: Genome, Fungal, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Chromosome organization, Chromosomes, Fungal, Genome, Fungal, General Agricultural and Biological Sciences, MESH: Genes, Fungal, 3C, ARS, Developmental Biology, Biotechnology, Research Article
Abstract: Background The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments. Results We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus. Conclusions Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0177-6) contains supplementary material, which is available to authorized users.
Published: 2015

22. A FACS-optimized screen identifies regulators of genome stability in Candida albicans

Author: Mélanie Legrand, Raphaël Loll-Krippleber, Adeline Feri, Marie Nguyen, Corinne Maufrais, Christophe d'Enfert, Jennifer Yansouni, Université Paris Diderot - Paris 7 (UPD7), Biologie et Pathogénicité fongiques, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], Cytométrie (Plate-forme), Institut Pasteur [Paris], Centre d'Informatique pour la Biologie, PT Génomique et Transcriptomique, BIOASTER, Lyon, This work was supported by the French Government's Investissement d'Avenir program, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID). R.L.-K. was the recipient of a Ph.D. grant from INRA and the Institut Pasteur. M.L. was the recipient of a postdoctoral fellowship from the Institut Pasteur (Bourse Roux)., ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), BIOASTER Microbiology Technology Institute [Lyon], ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)
Subjects: Genome instability, Locus (genetics), Microbiology, Genomic Instability, Loss of heterozygosity, Fungal Proteins, Candida albicans, MESH: Cloning, Molecular, Cloning, Molecular, Molecular Biology, Gene, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, Fungal protein, biology, MESH: Candida albicans, MESH: Genomic Instability, General Medicine, Articles, G2-M DNA damage checkpoint, biology.organism_classification, Corpus albicans, MESH: Genome, Fungal, MESH: Fungal Proteins, Genome, Fungal
Abstract: Loss of heterozygosity (LOH) plays important roles in genome dynamics, notably, during tumorigenesis. In the fungal pathogen Candida albicans , LOH contributes to the acquisition of antifungal resistance. In order to investigate the mechanisms that regulate LOH in C. albicans , we have established a novel method combining an artificial heterozygous locus harboring the blue fluorescent protein and green fluorescent protein markers and flow cytometry to detect LOH events at the single-cell level. Using this fluorescence-based method, we have confirmed that elevated temperature, treatment with methyl methanesulfonate, and inactivation of the Mec1 DNA damage checkpoint kinase triggered an increase in the frequency of LOH. Taking advantage of this system, we have searched for C. albicans genes whose overexpression triggered an increase in LOH and identified four candidates, some of which are known regulators of genome dynamics with human homologues contributing to cancer progression. Hence, the approach presented here will allow the implementation of new screens to identify genes that are important for genome stability in C. albicans and more generally in eukaryotic cells.
Published: 2015

23. Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium

Author: Jean-Marc Jeltsch, Vincent Phalip, Didier Hatsch, Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Cellulose 1,4-beta-Cellobiosidase, MESH: DNA Topoisomerases, Type II, DNA, Ribosomal, Polymerase Chain Reaction, Microbiology, chemistry.chemical_compound, Fusarium, Phylogenetics, Cellulose 1,4-beta-Cellobiosidase, MESH: Phylogeny, Molecular Biology, Genotyping, Gene, Phylogeny, MESH: DNA, Intergenic, Genetics, MESH: Fusarium, MESH: DNA, Ribosomal, biology, Phylogenetic tree, Intron, MESH: Polymerase Chain Reaction, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, biology.organism_classification, Fusarium sporotrichioides, DNA Topoisomerases, Type II, chemistry, MESH: Genome, Fungal, DNA, Intergenic, Genome, Fungal, Fusarium solani, DNA
Abstract: Molecular identification and phylogenetic studies rely to a large extent on rDNA sequence polymorphism. In the field of fungal taxonomy, despite the use of huge amounts of rDNA data available, some species within a given genus remain indistinguishable. Therefore, new target sequences need to be selected and validated. This is the case for Fusarium, which includes numerous species most of which are involved in both animal and plant pathologies. In addition to the rDNA fragment encompassing the internal transcribed spacers ITS1 and ITS2 and the 5.8 S sequence, two newly characterized genes were used as molecular markers for Fusarium species genotyping. The cellobiohydrolase-C (cbh-C) and the topoisomerase II (topII) gene parts were cloned and sequenced for at least one isolate of each of the eleven different species of our collection. Both cbh-C and topII were found to be single copy genes. DNA fragments amplified by PCR in order to establish phylogenetic trees range from 1123 to 1157 bp for rDNA and from 327 to 344 bp for cbh-C (this part contains one intron). The topII gene part encoding the carboxy-terminus of the ATP binding domain of the enzyme is constant in length with a value of 724 bp. PAUP-generated phylogenetic analyses based either on cbh-C or topII data enabled all species to be distinguished, and were more informative than those resulting from rDNA sequences. Furthermore, a combination of the three datasets enhanced the accuracy of the analyses and open up new possibilities for rapid molecular identification and evolution studies within the Fusarium genus.
Published: 2004

24. Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny

Author: Laurence Despons, Véronique Leh-Louis, S. Wain‐Hobson, Serge Potier, Jean Luc Souciet, Bénédicte Wirth, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Rétrovirologie Moléculaire, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Saccharomyces cerevisiae Proteins, Sequence analysis, Molecular Sequence Data, Saccharomyces cerevisiae, Biology, MESH: Tandem Re, MESH: Research Support, Non-U.S. Gov't, Genome, Evolution, Molecular, 03 medical and health sciences, MESH: Saccharomyces cerevisiae Proteins, Tandem repeat, Phylogenetics, Sequence Homology, Nucleic Acid, Genetics, ORFS, DNA, Fungal, Gene, MESH: Evolution, Molecular, Phylogeny, 030304 developmental biology, Synteny, Recombination, Genetic, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, MESH: Conserved Sequence, MESH: Molecular Sequence Data, Base Sequence, 030306 microbiology, MESH: Gene Duplication, Fungal genetics, Chromosome Mapping, MESH: Synteny, Articles, Sequence Analysis, DNA, MESH: RNA, Transfer, MESH: Chromosomes, Fungal, Multigene Family, MESH: Genome, Fungal, Mutation, MESH: RNA, Ribosomal, MESH: Genes, Fungal
Abstract: Multigene families are observed in all genomes sequenced so far and are the reflection of key evolutionary mechanisms. The DUP240 family, identified in Saccharomyces cerevisiae strain S288C, is composed of 10 paralogs: seven are organized as two tandem repeats and three are solo ORFs. To investigate the evolution of the three solo paralogs, YAR023c, YCR007c and YHL044w, we performed a comparative analysis between 15 S.cerevisiae strains. These three ORFs are present in all strains and the conservation of synteny indicates that they are not frequently involved in chromosomal reshaping, in contrast to the DUP240 ORFs organized in tandem repeats. Our analysis of nucleotide and amino acid variations indicates that YAR023c and YHL044w fix mutations more easily than YCR007c, although they all belong to the same multigene family. This comparative analysis was also conducted with five arbitrarily chosen Ascomycetes-specific genes and five arbitrarily chosen common genes (genes that have a homolog in at least one non-Ascomycetes organism). Ascomycetes-specific genes appear to be diverging faster than common genes in the S.cerevisiae species, a situation that was previously described between different yeast species. Our results point to the strong contribution, during DNA sequence evolution, of allelic recombination besides nucleotide substitution.
Published: 2004

25. yMGV: helping biologists with yeast microarray data mining

Author: Philippe Marc, Frédéric Devaux, Claude Jacq, Stéphane Le Crom, Régulation de l'expression génétique (REG), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), inconnu temporaire UPEMLV, Inconnu, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Information Storage and Retrieval, Genome, MESH: Down-Regulation, Transcriptome, Gene Expression Regulation, Fungal, Yeasts, Databases, Genetic, Gene cluster, MESH: Up-Regulation, Microarray databases, MESH: Databases, Genetic, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, Fungal protein, MESH: Yeasts, 030302 biochemistry & molecular biology, Telomere, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Up-Regulation, MESH: Internet, Multigene Family, MESH: Genome, Fungal, MESH: Fungal Proteins, MESH: Computer Graphics, Genome, Fungal, DNA microarray, MESH: Gene Expression Regulation, Fungal, MESH: Forecasting, Genes, Fungal, Down-Regulation, Computational biology, Biology, Article, Fungal Proteins, MESH: Gene Expression Profiling, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Computer Graphics, 030304 developmental biology, Internet, Microarray analysis techniques, Gene Expression Profiling, MESH: Information Storage and Retrieval, Gene expression profiling, MESH: Oligonucleotide Array Sequence Analysis, MESH: Multigene Family, Database Management Systems, MESH: Genes, Fungal, MESH: Telomere, MESH: Database Management Systems, Forecasting
Abstract: International audience; yMGV (yeast Microarray Global Viewer) was designed to provide biologists with meaningful information from genome-wide yeast expression data. The database includes most of the available expression data published on yeast microarrays over the last 4 years. It provides customizable tools for the rapid visualization of expression profiles associated with a set of genes from all published experiments. It also allows users to compare the results from different publications so that they can identify genes with common expression profiles. We used yMGV to perform global analyses to find a gene expression profile specific for given biological conditions and to locate functional gene clusters on chromosomes. Other organisms will be added to this database. yMGV is accessible on the web at http://transcriptome.ens.fr/ymgv.
Published: 2002

26. Replication origin selection regulates the distribution of meiotic recombination

Author: Pei-Yun Jenny Wu, Paul Nurse, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Rockefeller University [New York], The Francis Crick Institute [London], Women and Science Foundation, Fondation pour la Recherche Medicale, CNRS/INSERM (ATIP-Avenir), Breast Cancer Research Foundation, Anderson Center for Cancer Research, Wellcome Trust [093917], Rockefeller University, Martin, Clémence, Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: RAD51, MESH: Cell Cycle, MESH: DNA Replication, Pre-replication complex, S Phase, DNA replication factor CDT1, INITIATION, MESH: Protein Structure, Tertiary, Gene Expression Regulation, Fungal, PROGRAM, MESH: Replication Origin, MESH: Rad51 Recombinase, Promoter Regions, Genetic, Oligonucleotide Array Sequence Analysis, Recombination, Genetic, Genetics, MESH: Chromatin Immunoprecipitation, Cell Cycle, MESH: S Phase, Nuclear Proteins, MEIOSIS, DNA-Binding Proteins, S-PHASE, MESH: Schizosaccharomyces, MESH: Genome, Fungal, MESH: Recombination, Genetic, Genome, Fungal, MESH: Gene Expression Regulation, Fungal, DNA Replication, Chromatin Immunoprecipitation, BREAKS, Replication Origin, FISSION YEAST, Biology, Short Article, Meiosis, Schizosaccharomyces, MESH: Promoter Regions, Genetic, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, DNA replication, DNA-REPLICATION, MESH: Schizosaccharomyces pombe Proteins, Cell Biology, GENE, Protein Structure, Tertiary, YEAST SCHIZOSACCHAROMYCES-POMBE, MESH: Meiosis, Licensing factor, MESH: Oligonucleotide Array Sequence Analysis, biology.protein, Origin recognition complex, Rad51 Recombinase, Schizosaccharomyces pombe Proteins, sense organs, Homologous recombination, MESH: Nuclear Proteins, MESH: DNA-Binding Proteins
Abstract: Summary The program of DNA replication, defined by the temporal and spatial pattern of origin activation, is altered during development and in cancers. However, whether changes in origin usage play a role in regulating specific biological processes remains unknown. We investigated the consequences of modifying origin selection on meiosis in fission yeast. Genome-wide changes in the replication program of premeiotic S phase do not affect meiotic progression, indicating that meiosis neither activates nor requires a particular origin pattern. In contrast, local changes in origin efficiencies between different replication programs lead to changes in Rad51 recombination factor binding and recombination frequencies in these domains. We observed similar results for Rad51 when changes in efficiencies were generated by directly targeting expression of the Cdc45 replication factor. We conclude that origin selection is a key determinant for organizing meiotic recombination, providing evidence that genome-wide modifications in replication program can modulate cellular physiology., Graphical Abstract, Highlights • Premeiotic S phase neither activates nor requires a specific origin usage program • Origin selection is a key regulator of the distribution of meiotic recombination • Organization of genome duplication has a functional impact on cellular physiology, Changes in the pattern of DNA replication are observed during development and in various pathologies, but it is unclear whether they contribute to these processes. Wu and Nurse show, by altering replication origin usage in fission yeast, that origin selection is critical for the organization of meiotic recombination.
Published: 2014

27. The fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

Author: David R. Nelson, Hans-Werner Mewes, H. Corby Kistler, Weihong Qi, Kerry O'Donnell, John C. Kennell, Scott E. Baker, Liane R. Gale, Igor V. Tetko, Jon K. Magnuson, Gary J. Muehlbauer, Martin Münsterkötter, Martijn Rep, Karen Hilburn, Jiqiang Yao, B. Gillian Turgeon, Thérèse Ouellet, Hadi Quesneville, Li-Jun Ma, Todd J. Ward, Linda J. Harris, Gerhard Adam, Kim E. Hammond-Kosack, Sarah E. Calvo, Scott Kroken, M. Isabel G. Roncero, Kye Yong Seong, Jin-Rong Xu, Gertrud Mannhaupt, Yueh-Long Chang, Antonio Di Pietro, Ulrich Güldener, Christina A. Cuomo, Evan Mauceli, Rudolf Mitterbauer, John F. Antoniw, Rubella S. Goswami, David DeCaprio, Martin Urban, Cees Waalwijk, Jonathan D. Walton, Sante Gnerre, Frances Trail, Thomas K. Baldwin, Bruce W. Birren, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Purdue University [West Lafayette], Michigan State University [East Lansing], Michigan State University System, Cornell University [New York], Universidad de Córdoba [Cordoba], Pacific Northwest National Laboratory (PNNL), University of Amsterdam [Amsterdam] (UvA), Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Rothamsted Research, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Agriculture and Agri-Food [Ottawa] (AAFC), U.S. Department of Agriculture - Agricultural Research Service - Cereal Disease Laboratory (USDA), USDA-ARS : Agricultural Research Service, Saint Louis University (SLU), University of Arizona, University of Tennessee Memphis, The University of Tennessee Health Science Center [Memphis] (UTHSC), USDA ARS, National Center for Agricultural Utilization Research (USDA ARS,), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institute of Bioorganic Chemistry and Photochemistry, National Ukrainian Academy of Sciences, Institute Bioorganic Chemistry an Photochemistry, Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), Molecular Plant Pathology (SILS, FNWI), Technische Universität München [München] (TUM), Cornell University, University of Minnesota [Twin Cities], and Wageningen University and Research Centre [Wageningen] (WUR)
Subjects: localized polymorphism, MESH: Sequence Analysis, DNA, neurospora, Sequence analysis, Molecular Sequence Data, Single-nucleotide polymorphism, Genomics, Gene mutation, Biology, dna, medicine.disease_cause, Genome, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, MESH: Plant Diseases, Fusarium, MESH: Polymorphism, Genetic, medicine, Point Mutation, DNA, Fungal, Gene, MESH: Evolution, Molecular, 030304 developmental biology, Plant Diseases, MESH: Point Mutation, Genetics, 0303 health sciences, Mutation, MESH: Fusarium, Multidisciplinary, Polymorphism, Genetic, MESH: Molecular Sequence Data, Biointeracties and Plant Health, 030306 microbiology, Point mutation, MESH: Polymorphism, Single Nucleotide, food and beverages, Hordeum, Sequence Analysis, DNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: DNA, Fungal, MESH: Hordeum, MESH: Genome, Fungal, Fusarium graminearum genome, PRI Biointeractions en Plantgezondheid, Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum , a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.
Published: 2007

28. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies 1 1Edited by G. von Heijne

Author: J. van Helden, Julio Collado-Vides, Bruno André, Université libre de Bruxelles (ULB), Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México (UNAM), and Département de Biologie Moléculaire, Université Libre de Bruxelles
Subjects: MESH: Computers, Saccharomyces cerevisiae, MESH: Algorithms, 03 medical and health sciences, 0302 clinical medicine, Structural Biology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Regulatory Sequences, Nucleic Acid, MESH: Computer Communication Networks, Molecular Biology, Gene, 030304 developmental biology, Genetics, [STAT.AP]Statistics [stat]/Applications [stat.AP], 0303 health sciences, biology, Oligonucleotide, MESH: Transcription Factors, biology.organism_classification, MESH: Saccharomyces cerevisiae, DNA binding site, Regulon, MESH: Binding Sites, Regulatory sequence, MESH: Genome, Fungal, Multiple EM for Motif Elicitation, MESH: Oligodeoxyribonucleotides, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Genes, Fungal, Functional genomics, MESH: DNA-Binding Proteins, MESH: Gene Expression Regulation, Fungal, 030217 neurology & neurosurgery
Abstract: International audience; We present here a simple and fast method allowing the isolation of DNA binding sites for transcription factors from families of coregulated genes, with results illustrated in Saccharomyces cerevisiae. Although conceptually simple, the algorithm proved efficient for extracting, from most of the yeast regulatory families analyzed, the upstream regulatory sequences which had been previously found by experimental analysis. Furthermore, putative new regulatory sites are predicted within upstream regions of several regulons. The method is based on the detection of over-represented oligonucleotides. A specificity of this approach is to define the statistical significance of a site based on tables of oligonucleotide frequencies observed in all non-coding sequences from the yeast genome. In contrast with heuristic methods, this oligonucleotide analysis is rigorous and exhaustive. Its range of detection is however limited to relatively simple patterns: short motifs with a highly conserved core. These features seem to be shared by a good number of regulatory sites in yeast. This, and similar methods, should be increasingly required to identify unknown regulatory elements within the numerous new coregulated families resulting from measurements of gene expression levels at the genomic scale. All tools described here are available on the web at the site http://copan.cifn.unam.mx/Computational_Biology/ yeast-tools
Published: 1998

29. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens

Author: Pierre Legrain, Micheline Fromont-Racine, Jean-Christophe Rain, Métabolisme des ARN, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by the European Union (Biotech 95007-the TAPIR network-and CHRX-CT94-0677), the Ministere de la Recherche (ACC-SVJ) and the Fondation pour la Recherche Medicale., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: RNA Splicing, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Saccharomyces cerevisiae, MESH: Sequence Alignment, Sequence alignment, MESH: Amino Acid Sequence, ENCODE, Genome, Fungal Proteins, Open Reading Frames, 03 medical and health sciences, Genetics, Genomic library, Amino Acid Sequence, Gene, Crosses, Genetic, 030304 developmental biology, Genomic Library, 0303 health sciences, MESH: Molecular Sequence Data, biology, MESH: Ribonucleoproteins, Small Nuclear, 030302 biochemistry & molecular biology, MESH: Genomic Library, MESH: Open Reading Frames, Ribonucleoproteins, Small Nuclear, biology.organism_classification, MESH: Crosses, Genetic, MESH: Saccharomyces cerevisiae, Yeast, MESH: Genetic Techniques, Genetic Techniques, MESH: Genome, Fungal, RNA splicing, MESH: Fungal Proteins, Genome, Fungal, MESH: RNA Splicing, Sequence Alignment
Abstract: International audience; The genome of the yeast Saccharomyces cerevisiae is now completely sequenced. Despite successful genetic work in recent years, 60% of yeast genes have no assigned function and half of those encode putative proteins without any homology with known proteins. Genetic analyses, such as suppressor or synthetic lethal screens, have suggested many functional links between gene products, some of which have been confirmed by biochemical means. Altogether, these approaches have led to a fairly extensive knowledge of defined biochemical pathways. However, the integration of these pathways against the background of complexity in a living cell remains to be accomplished. The two-hybrid method applied to the yeast genome might allow the characterization to the network of interactions between yeast proteins, leading to a better understanding of cellular functions. Such an analysis has been performed for the bacteriophage T7 genome that encodes 55 proteins and for Drosophila cell cycle regulators. However, the currently available two-hybrid methodology is not suitable for a large-scale project without specific methodological improvements In particular, the exhaustivity and selectivity of the screens must first be greatly improved. We constructed a new yeast genomic library and developed a highly selective two-hybrid procedure adapted for exhaustive screens of the yeast genome. For each bait we selected a limited set of interacting preys that we classified in categories of distinct heuristic values. Taking into account this classification, new baits were chosen among preys and, in turn, used for second-round screens. Repeating this procedure several times led to the characterization of the network of interactions. Using known pre-mRNA splicing factors as initial baits, we were able to characterize new interactions between known splicing factors, identify new yeast splicing factors, including homologues of human SF1 and SAP49, and reveal novel potential functional links between cellular pathways. Using different cellular pathways as anchor points, this novel strategy allows us to envision the building of an interaction map of the yeast proteome. In addition, this two-hybrid strategy could be applied to other genomes and might help to resolve the human protein linkage map.
Published: 1997

30. Candida albicans is not always the preferential yeast colonizing humans: a study in Wayampi Amerindians

Author: Mouna Ben Soltana, Laure Diancourt, Antoine Andremont, Paul-Louis Woerther, Sophie Abélanet, Félix Djossou, Emmanuelle Permal, Cécile Angebault, Christiane Bouchier, Christophe d'Enfert, François Catzeflis, Marie-Elisabeth Bougnoux, CHU Necker - Enfants Malades [AP-HP], Université Paris Descartes - Paris 5 (UPD5), Laboratoire de bactériologie, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7), Biologie et Pathogénicité fongiques, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], Unité des Maladies Infectieuses et Tropicales [Cayenne, Guyanne Française], Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Institut Pasteur [Paris], Génomique (Plate-Forme), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), The ERAES project was supported in part by the Agence Française de Sécurité Sanitaire de l’Environnement et du Travail(contracts ES-05-01 and EST-09-21), the Agence Nationale pour la Recherche (contract 05-9-114), the Institut National de la Santé et de la Recherche Médicale (INSERM, contracts C06-18 and C10-19), the Centre National de Référence' Résistance bactérienne dans les flores commensales, 'the Fondation pour la Recherche Médicale (grants FDM20090615761 andFDM20100619023 to C. A.), and the French government ’ s Investissement d'Avenir program, Laboratoire d’Excellence'Integrative Biology of Emerging Infectious Diseases' (grant ANR-10-LABX-62-IBEID), ANR: the Agence Nationale pour la Recher- che (contract 05-9-114),the Agence Nationale pour la Recher- che (contract 05-9-114),05-9-114 the Agence Nationale pour la Recher- che (contract 05-9-114), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Assistance publique - Hôpitaux de Paris (AP-HP) - AP-HP - Hôpital Bichat - Claude Bernard [Paris] - Université Paris Diderot - Paris 7 (UPD7), Institut National de la Recherche Agronomique (INRA) - Institut Pasteur [Paris], Institut des Sciences de l'Evolution de Montpellier (ISEM), Université de Montpellier (UM) - Institut de recherche pour le développement [IRD] : UR226 - Centre National de la Recherche Scientifique (CNRS), ANR : the Agence Nationale pour la Recher- che (contract 05-9-114), the Agence Nationale pour la Recher- che (contract 05-9-114), 05-9-114 the Agence Nationale pour la Recher- che (contract 05-9-114), ANR-10-LABX-62-IBEID, IBEID, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Génomique (Plate-Forme) - Genomics Platform, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 05-9-114 the Agence Nationale pour la Recher- che (contract 05-9-114) the Agence Nationale pour la Recher- che (contract 05-9-114), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: Male, MESH : Prevalence, MESH : Multilocus Sequence Typing, MESH : Aged, MESH : Candidiasis, MESH: Aged, 80 and over, Prevalence, Immunology and Allergy, Colonization, MESH : Female, MESH: Animals, Candida albicans, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Aged, 80 and over, 2. Zero hunger, MESH : Intestines, MESH: Aged, 0303 health sciences, MESH: Middle Aged, biology, MESH: Yeasts, Candidiasis, intestinal colonization, Middle Aged, MESH : Adult, Corpus albicans, MESH: Candidiasis, French Guiana, Intestines, Infectious Diseases, MESH : Carrier State, MESH: Multilocus Sequence Typing, whole-genome sequencing, MESH: Young Adult, Carrier State, MESH: Genome, Fungal, Female, Genome, Fungal, MESH: Carrier State, MLST, MESH: Intestines, Adult, MESH : French Guiana, Adolescent, Human intestine, MESH : Candida albicans, MESH : Male, Saccharomyces cerevisiae, MESH : Young Adult, yeasts, Microbiology, Evolution, Molecular, Young Adult, 03 medical and health sciences, MESH: Mycoses, Candida krusei, MESH : Adolescent, MESH: French Guiana, Animals, Humans, MESH : Middle Aged, MESH : Evolution, Molecular, MESH : Aged, 80 and over, MESH: Prevalence, Aged, 030304 developmental biology, MESH : Mycoses, MESH: Adolescent, MESH : Yeasts, MESH: Humans, 030306 microbiology, amerindians, MESH : Genome, Fungal, MESH: Candida albicans, MESH : Humans, MESH : Phylogeny, MESH: Adult, biology.organism_classification, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Yeast, MESH: Male, Carriage, Mycoses, candida albicans, MESH : Animals, MESH: Female, Multilocus Sequence Typing
Abstract: Chantier qualité GA; International audience; In industrialized countries Candida albicans is considered the predominant commensal yeast of the human intestine, with approximately 40% prevalence in healthy adults. We discovered a highly original colonization pattern that challenges this current perception by studying in a 4- year interval a cohort of 151 Amerindians living in a remote community (French Guiana), and animals from their environment. The prevalence of C. albicans was persistently low (3% and 7% of yeast carriers). By contrast, Candida krusei and Saccharomyces cerevisiae were detected in over 30% of carriers. We showed that C. krusei and S. cerevisiae carriage was of food or environmental origin, whereas C. albicans carriage was associated with specific risk factors (being female and living in a crowded household). We also showed using whole-genome sequence comparison that C. albicans strains can persist in the intestinal tract of a healthy individual over a 4-year period.
Published: 2013

31. Detection and characterization of megasatellites in orthologous and nonorthologous genes of 21 fungal genomes

Author: Fredj Tekaia, Guy-Franck Richard, Bernard Dujon, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported by ANR blanc 2011 (DYGEVO) and by Institut Pasteur (PTR370 to F.T ), ANR-11-BSV6-0001,DYGEVO,Dynamique et évolution des génomes de levures, modèles eucaryotes unicellulaires.(2011), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Threonine, [SDV]Life Sciences [q-bio], Molecular Sequence Data, MESH: Sequence Alignment, Sequence alignment, MESH: Amino Acid Sequence, MESH: Ascomycota, Biology, ENCODE, Microbiology, Genome, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, MESH: Protein Structure, Tertiary, Tandem repeat, Ascomycota, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Amino Acid Sequence, MESH: Threonine, MESH: Phylogeny, Molecular Biology, Gene, Phylogeny, MESH: Evolution, Molecular, 030304 developmental biology, Genetics, 0303 health sciences, Fungal protein, MESH: Molecular Sequence Data, Basidiomycota, 030302 biochemistry & molecular biology, General Medicine, Articles, Protein Structure, Tertiary, MESH: Tandem Repeat Sequences, MESH: Basidiomycota, Tandem Repeat Sequences, Multigene Family, MESH: Genome, Fungal, MESH: Multigene Family, MESH: Fungal Proteins, Genome, Fungal, Sequence Alignment, Function (biology)
Abstract: Megasatellites are large DNA tandem repeats, originally described in Candida glabrata , in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
Published: 2013

32. Mycorrhiza for all: an under-earth revolution

Author: Alice Vayssières, Laura B. Martínez-García, Edith C. Hammer, Kevin Garcia, Manaaki Whenua – Landcare Research [Lincoln], Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Freie Universität Berlin, Landcare Research, Ecosystem & Global Change, and Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Evolution, Physiology, Biogeography, MESH: Forestry, Plant Science, 01 natural sciences, 03 medical and health sciences, Symbiosis, Mycorrhizal fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Community ecology, Mycorrhiza, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, MESH: Humans, MESH: Symbiosis, biology, Community, Ecology, Agriculture, Genomics, biology.organism_classification, symbiosis, mycorrhizal fungi, MESH: Soil Microbiology, MESH: Genome, Fungal, MESH: Conservation of Natural Resources, Earth (chemistry), Inoculum, fungi, MESH: Mycorrhizae, MESH: Agriculture, 010606 plant biology & botany
Abstract: International audience
Published: 2013

33. Annotation of microsporidian genomes using transcriptional signals

Author: Ivan Wawrzyniak, Sébastien Terrat, Olivier Gonçalves, Nicolas Parisot, Pierre Peyret, Patrick Wincker, Corinne Biderre-Petit, Simone Duprat, Frédéric Delbac, Jean Weissenbach, Sébastien Rimour, Eric Dugat-Bony, Antoine Mahul, Gaelle Samson, Brigitte Chebance, Stéphanie Bornes, Jérémie Denonfoux, Eric Peyretaillade, Michael Katinka, Valérie Polonais, Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Agroécologie [Dijon], Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes ( LIMOS ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Sigma CLERMONT ( Sigma CLERMONT ) -Centre National de la Recherche Scientifique ( CNRS ), Génie Biologie, Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Genomic platform and R&D, GenoScreen, Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre Régional de Ressources Informatiques (CRRI), Clermont Université, Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), IUT Génie Biologique, Laboratoire de Biologie, Université d'Auvergne (Clermont Ferrand 1) (UdA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure des Mines de St Etienne, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Transcription, Genetic, genome annotation, MESH : Molecular Sequence Annotation, General Physics and Astronomy, MESH: Phosphotransferases, Genome, transcriptional signal, MESH : Protein Transport, MESH : Fungal Proteins, DNA, Fungal, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, Fungal protein, MESH: Conserved Sequence, Multidisciplinary, MESH: Genomics, 030302 biochemistry & molecular biology, Genomics, Genome project, Protein Transport, Molecular Sequence Annotation, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Genome, Fungal, MESH: Fungal Proteins, MESH : Phosphotransferases, Genome, Fungal, Transposable element, MESH: Protein Transport, Genes, Fungal, MESH: Molecular Sequence Annotation, MESH : Microsporidia, MESH : Open Reading Frames, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Fungal Proteins, Open Reading Frames, 03 medical and health sciences, MESH : Conserved Sequence, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Anncaliia algerae, parasitic diseases, Gene, 030304 developmental biology, bioinformatic, MESH: Transcription, Genetic, MESH : Genome, Fungal, Phosphotransferases, structural annotation, MESH : Genomics, fungi, MESH : Transcription, Genetic, General Chemistry, MESH: Open Reading Frames, MESH: Microsporidia, MESH: DNA, Fungal, microsporidia, MESH : Genes, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH : DNA, Fungal, MESH: Genes, Fungal
Abstract: EA GenoSol CT3; International audience; High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidian-host relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. Such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.
Published: 2012

34. Sodium selenide toxicity is mediated by O2-dependent DNA breaks

Author: Cosmin Saveanu, Pierre Plateau, Christophe Malabat, Myriam Lazard, Laurence Decourty, Alain Jacquier, Gérald Peyroche, Sylvain Blanquet, Marc Dauplais, François Beuneu, Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Génétique des Interactions Macromoléculaires, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Solides Irradiés (LSI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)
Subjects: MESH: Cell Death, Anatomy and Physiology, Yeast and Fungal Models, Haploidy, Toxicology, MESH: G2 Phase Cell Cycle Checkpoints, Gene Knockout Techniques, chemistry.chemical_compound, 0302 clinical medicine, Molecular Cell Biology, Mannitol, Anaerobiosis, Homologous Recombination, Selenium Compounds, Cellular Stress Responses, MESH: Gene Knockout Techniques, 0303 health sciences, Multidisciplinary, Cell Death, biology, Sodium selenide, Genomics, MESH: Haploidy, MESH: Saccharomyces cerevisiae, Aerobiosis, Functional Genomics, G2 Phase Cell Cycle Checkpoints, Biochemistry, 030220 oncology & carcinogenesis, MESH: Genome, Fungal, Medicine, MESH: Mannitol, Genome, Fungal, MESH: Oxygen, Research Article, Cell Physiology, DNA damage, MESH: Hypersensitivity, Science, Toxic Agents, chemistry.chemical_element, Saccharomyces cerevisiae, Mycology, Microbiology, Superoxide dismutase, MESH: Homologous Recombination, 03 medical and health sciences, Model Organisms, Genome Analysis Tools, MESH: Aerobiosis, Hydrogen selenide, MESH: Anaerobiosis, Hypersensitivity, Genome-Wide Association Studies, MESH: Chromosome Aberrations, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, DNA Breaks, Single-Stranded, Fragmentation (cell biology), Biology, 030304 developmental biology, Chromosome Aberrations, MESH: DNA Breaks, Single-Stranded, MESH: Selenium Compounds, G2-M DNA damage checkpoint, Yeast, Oxygen, chemistry, biology.protein, Hydroxyl radical, Selenium
Abstract: International audience; Hydrogen selenide is a recurrent metabolite of selenium compounds. However, few experiments studied the direct link between this toxic agent and cell death. To address this question, we first screened a systematic collection of Saccharomyces cerevisiae haploid knockout strains for sensitivity to sodium selenide, a donor for hydrogen selenide (H(2)Se/HSe(-/)Se(2-)). Among the genes whose deletion caused hypersensitivity, homologous recombination and DNA damage checkpoint genes were over-represented, suggesting that DNA double-strand breaks are a dominant cause of hydrogen selenide toxicity. Consistent with this hypothesis, treatment of S. cerevisiae cells with sodium selenide triggered G2/M checkpoint activation and induced in vivo chromosome fragmentation. In vitro, sodium selenide directly induced DNA phosphodiester-bond breaks via an O(2)-dependent reaction. The reaction was inhibited by mannitol, a hydroxyl radical quencher, but not by superoxide dismutase or catalase, strongly suggesting the involvement of hydroxyl radicals and ruling out participations of superoxide anions or hydrogen peroxide. The (*)OH signature could indeed be detected by electron spin resonance upon exposure of a solution of sodium selenide to O(2). Finally we showed that, in vivo, toxicity strictly depended on the presence of O(2). Therefore, by combining genome-wide and biochemical approaches, we demonstrated that, in yeast cells, hydrogen selenide induces toxic DNA breaks through an O(2)-dependent radical-based mechanism.
Published: 2012

35. Insights into the life cycle of yeasts from the CTG clade revealed by the analysis of the [i]Millerozyma (Pichia) farinosa[/i] species complex

Author: Christine Sacerdot, Véronique Leh-Louis, Serge Casaregola, Noémie Jacques, Sandrine Mallet, Stéphanie Weiss, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-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), AIP Bioresources INRA grant, European Community [FP7-228310], and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Applied Microbiology, [SDV]Life Sciences [q-bio], lcsh:Medicine, Haploidy, MESH: Reproduction, Fungal Evolution, MESH: Animals, lcsh:Science, Clade, DNA, Fungal, MESH: Phylogeny, Genome Evolution, Phylogeny, MESH: Chimera, Genetics, 0303 health sciences, Multidisciplinary, Phylogenetic tree, Reproduction, Reproductive isolation, Genomics, MESH: Haploidy, Spores, Fungal, MESH: Chromosomes, Fungal, Phylogenetics, MESH: Reproducibility of Results, MESH: Cattle, MESH: Genome, Fungal, Ploidy, Chromosomes, Fungal, Genome, Fungal, Research Article, Biotechnology, Mitochondrial DNA, Species complex, Sequence analysis, Introgression, Mycology, Biology, Microbiology, DNA, Mitochondrial, 03 medical and health sciences, MESH: Spores, Fungal, MESH: Aneuploidy, Animals, Humans, Evolutionary Systematics, MESH: Saccharomycetales, MESH: Life Cycle Stages, 030304 developmental biology, Evolutionary Biology, Life Cycle Stages, MESH: Humans, 030306 microbiology, Chimera, lcsh:R, MESH: DNA, Mitochondrial, Reproducibility of Results, Genomic Evolution, Comparative Genomics, Aneuploidy, Yeast, MESH: DNA, Fungal, Fungal Classification, Saccharomycetales, lcsh:Q, Cattle
Abstract: Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004(T) ( = CLIB 1230(T)) and Candida pseudofarinosa sp. nov.NCYC 386(T)( = CLIB 1231(T)). Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strains from distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity.
Published: 2012

36. CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR

Author: Benoit Arcangioli, Stephen Watt, Jürg Bähler, Derek B. Goto, Matthew W. Vaughn, Robert A. Martienssen, Danielle V. Irvine, Mikel Zaratiegui, Cold Spring Harbor Laboratory (CSHL), University College of London [London] (UCL), UCL Cancer Institute, Dynamique du Génome, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by National Institutes of Health grant RO1GM076396 to R.A.M., Cancer Research UK grant C9546/A6517 to J.B., l’Agence Nationale de la Recherche grant ANR-06-BLAN-0271 to B.A., a National Health and Medical Research Council C.J. Martin Fellowship to D.V.I. and a Postdoctoral Fellowship from the Spanish Ministry of Education to M.Z., and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome instability, DNA Replication, Retroelements, Heterochromatin, Chromosomal Proteins, Non-Histone, Retrotransposon, MESH: DNA Replication, macromolecular substances, Article, Genomic Instability, 03 medical and health sciences, 0302 clinical medicine, MESH: Retroelements, MESH: Chromosomal Proteins, Non-Histone, Schizosaccharomyces, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Conserved Sequence, 030304 developmental biology, Genetics, Recombination, Genetic, MESH: DNA Damage, 0303 health sciences, Multidisciplinary, MESH: Conserved Sequence, biology, Chromosomal fragile site, MESH: Genomic Instability, DNA replication, Terminal Repeat Sequences, MESH: Schizosaccharomyces pombe Proteins, biology.organism_classification, Long terminal repeat, 3. Good health, DNA-Binding Proteins, Histone, MESH: Schizosaccharomyces, MESH: Terminal Repeat Sequences, Schizosaccharomyces pombe, MESH: Genome, Fungal, biology.protein, MESH: Recombination, Genetic, Schizosaccharomyces pombe Proteins, Genome, Fungal, Centromere Protein B, MESH: Centromere Protein B, 030217 neurology & neurosurgery, MESH: DNA-Binding Proteins, DNA Damage
Abstract: International audience; Centromere-binding protein B (CENP-B) is a widely conserved DNA binding factor associated with heterochromatin and centromeric satellite repeats. In fission yeast, CENP-B homologues have been shown to silence long terminal repeat (LTR) retrotransposons by recruiting histone deacetylases. However, CENP-B factors also have unexplained roles in DNA replication. Here we show that a molecular function of CENP-B is to promote replication-fork progression through the LTR. Mutants have increased genomic instability caused by replication-fork blockage that depends on the DNA binding factor switch-activating protein 1 (Sap1), which is directly recruited by the LTR. The loss of Sap1-dependent barrier activity allows the unhindered progression of the replication fork, but results in rearrangements deleterious to the retrotransposon. We conclude that retrotransposons influence replication polarity through recruitment of Sap1 and transposition near replication-fork blocks, whereas CENP-B counteracts this activity and promotes fork stability. Our results may account for the role of LTR in fragile sites, and for the association of CENP-B with pericentromeric heterochromatin and tandem satellite repeats.
Published: 2011

37. Exploring plant defense pathways in the carrot-Alternaria dauci pathosystem, a non-model interaction

Author: Lecomte, M., Allenda, C., Sement, F., Berthet, M., Briard, Mathilde, Hamama, L., Poupard, P., Berruyer, R., Génétique et Horticulture (GenHort), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: MESH: Alternaria, MESH: Genomics, food and beverages, Alternaria, Genomics, Daucus carota, MESH: DNA, Fungal, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, MESH: Plant Diseases, MESH: Daucus carota, MESH: Genome, Fungal, Genome, Fungal, DNA, Fungal, Plant Diseases
Abstract: Communication (Communication avec actes dans un congrès); Most of the molecular mechanisms underlying plant partial resistance QTLs are still unknown. Twocompeting hypothesis are generally invoked to link observed field resistance with actual moleculargene function. An older hypothesis links partial resistance QTLs with overcome typical R genesencoding classical NBS-LRR or LRR-TM type proteins. In a recent paper (Hu et al., 2008), partial plantresistance was linked with defense mechanisms. These results led us to develop a candidate geneapproach to study partial plant resistance of carrot (Daucus carota) towards its main foliar fungalpathogen, Alternaria dauci. Since carrot is a non-model plant, little sequence data is available onpublic databases. We thus chose to develop a homology-based cloning strategy in order to detectand sequence defense-related genes in carrot. Since A. dauci is a necrotrophic pathogen, we focusedthis strategy on Jasmonic acid (JA) signaling pathway and JA controlled defense genes (such as JAZ3or PR4). Since the degenerate primer strategy is not known to be effective on each and every gene,we chose to apply it in a parallel fashion on a rather large set of genes. Alignments of sequence datafrom eight already sequenced dicotyledonous plant species were performed for 15 genes.Degenerate primers were defined for 10 genes involved in this JA pathway. Additionally, we defineddegenerate primers for two defense genes that are not mainly JA- regulated: the SA-regulateddefense gene PR1, and the non host defense gene PAL1. Five out of 12 genes were partially clonedand sequenced. Two strategies are currently deployed to link these defense related genes withpartial resistance QTLs observed in the carrot-A. dauci interaction (Le Clerc et al., 2009). SNPs arebeing found between the resistant and susceptible parents of our mapping populations. They willhelp us to find potential QTL-candidate co-localizations. Absence of such a co-localization does notmean that a potential candidate is not involved in defense. It is also possible that the QTL influencesdefense-related genes activation rather than the efficiency of the cognate PR proteins. For thisreason, we also plan to study the induction of these genes by A. dauci in both susceptible andresistant backgrounds.
Published: 2011

38. Tracking of single and multiple genomic loci in living yeast cells

Author: Imen, Lassadi, Kerstin, Bystricky, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération ( LBCMCP ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de biologie moléculaire eucaryote du CNRS ( LBME ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire eucaryote (LBME), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microscopy, Confocal, MESH : Microscopy, Fluorescence, MESH : Genome, Fungal, MESH : Saccharomyces cerevisiae, MESH: Microscopy, Fluorescence, MESH: Polymerase Chain Reaction, Saccharomyces cerevisiae, Polymerase Chain Reaction, MESH: Saccharomyces cerevisiae, Microscopy, Fluorescence, MESH: Genome, Fungal, MESH: Microscopy, Confocal, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genome, Fungal, MESH : Microscopy, Confocal, MESH : Polymerase Chain Reaction, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract: International audience; Nuclear organization is involved in numerous aspects of cellular function. In yeast, analysis of the nuclear position and dynamics of the silent and active mating-type loci has allowed to gain insight into the mechanisms involved in directing mating-type switching. The fluorescent repressor operator systems (FROS) have proven to be a powerful technique to tag DNA sequences to investigate chromosome position and dynamics in living cells. FROS rely on the transgenic expression of a bacterial repressor fused to a fluorescent protein which can bind to its respective operator DNA sequence integrated as multicopy tandem arrays at a specific genomic site. Different FROS exist which facilitate the tagging of up to three different loci simultaneously. This chapter describes detailed protocols for FROS usage and analysis in the yeast Saccharomyces cerevisiae.
Published: 2011

39. Systems biology of infectious diseases: a focus on fungal infections

Author: Michael Bromley, Philippe Pierre, Ivo Gut, Lisa Rizzetto, Rodrigo Santamaría, Wanseon Lee, Duccio Cavalieri, Brian Miller, Misha Kapushesky, Teresa Zelante, Luigina Romani, Manuel A. S. Santos, Paul Bowyer, University of Salamanca - Spain, University of Salamanca, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), University of Manchester [Manchester], Università degli Studi di Perugia (UNIPG), European Bioinforrmatics Institute (UK) (EBI), École de biologie industrielle (EBI), AlerGenetica (UK), AlerGenetica, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universidade de Aveiro, Universidad de Salamanca, Università degli Studi di Firenze = University of Florence (UniFI), and Università degli Studi di Perugia = University of Perugia (UNIPG)
Subjects: Proteomics, Antifungal Agents, MESH: Th17 Cells, Disease, MESH: Drug Design, Bioinformatics, MESH: Receptors, Pattern Recognition, MESH: Molecular Targeted Therapy, Candida albicans, Immunology and Allergy, MESH: Animals, MESH: Immune Evasion, MESH: Genetic Variation, Molecular Targeted Therapy, Organism, MESH: Cytokines, 0303 health sciences, MESH: Proteomics, Systems Biology, Hematology, 3. Good health, Drug development, MESH: Systems Biology, Receptors, Pattern Recognition, MESH: Genome, Fungal, Host-Pathogen Interactions, MESH: Communicable Diseases, [SDV.IMM]Life Sciences [q-bio]/Immunology, Cytokines, MESH: Aspergillus fumigatus, Genome, Fungal, MESH: Immune Tolerance, Systems biology, Host–pathogen interaction, Immunology, Computational biology, Biology, Communicable Diseases, Underlying infection, 03 medical and health sciences, MESH: Mycoses, Immune Tolerance, Animals, Humans, Immune Evasion, 030304 developmental biology, MESH: Humans, 030306 microbiology, MESH: Candida albicans, Aspergillus fumigatus, MESH: Host-Pathogen Interactions, MESH: Biological Markers, Genetic Variation, Th1 Cells, MESH: Antifungal Agents, Microarray Analysis, MESH: Microarray Analysis, MESH: Th1 Cells, Mycoses, Infectious disease (medical specialty), Drug Design, Th17 Cells, Biomarkers
Abstract: International audience; The study of infectious disease concerns the interaction between the host species and a pathogen organism. The analysis of such complex systems is improving with the evolution of high-throughput technologies and advanced computational resources. This article reviews integrative, systems-oriented approaches to understanding mechanisms underlying infection, immune response and inflammation to find biomarkers of disease and design new drugs. We focus on the systems biology process, especially the data gathering and analysis techniques rather than the experimental technologies or latest computational resources.
Published: 2011

40. Extreme reduction and compaction of microsporidian genomes

Author: Hicham El Alaoui, Nicolas Parisot, David Biron, Frédéric Delbac, Eric Peyretaillade, Marie Diogon, Valérie Polonais, Pierre Peyret, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genome evolution, Transcription, Genetic, Bacterial genome size, Biology, Microbiology, Genome, Evolution, Molecular, 03 medical and health sciences, Gene density, parasitic diseases, MESH: Genetic Variation, MESH: Phylogeny, Molecular Biology, Gene, Genome size, Phylogeny, MESH: Evolution, Molecular, 030304 developmental biology, Genetics, 0303 health sciences, 030306 microbiology, MESH: Transcription, Genetic, fungi, MESH: Host-Pathogen Interactions, Fungal genetics, Genetic Variation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, MESH: Microsporidia, Host-Pathogen Interactions, Microsporidia, C-value, MESH: Genome, Fungal, Genome, Fungal
Abstract: International audience; Microsporidia are fungi-related obligate intracellular parasites with a highly reduced and compact genome, as for Encephalitozoon species which harbor a genome smaller than 3 Mbp. Genome compaction is reflected by high gene density and, for larger microsporidian genomes, size variation is due to repeat elements that do not drastically affect gene density. Furthermore, these pathogens present strong host dependency illustrated by extensive gene loss. Such adaptations associated with genome compaction induced gene size reduction but also simplification of cellular processes such as transcription. Thus, microsporidia are excellent models for eukaryotic genome evolution and gene expression in the context of host-pathogen relationships.
Published: 2011

41. The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

Author: Erzsébet Fekete, Lukas Hartl, Irina S. Druzhinina, Stéphane Le Crom, Lea Atanasova, Bernhard Seiboth, Erzsébet Sándor, Thomas Portnoy, Antoine Margeot, Levente Karaffa, Rita Linke, Christian P. Kubicek, BMC, Ed., IFP Energies nouvelles (IFPEN), GenomiqueENS (Genomique ENS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Austrian Center of Industrial Biotechnology [Vienna, Austria] (Institute of Chemical Engineering), Vienna University of Technology (TU Wien), Research Area Gene Technology and Applied Biochemistry [Vienna, Austria] (Institute of Chemical Engineering), Biochemical Engineering Department [Debrecen, Hungary] (Faculty of Science & Technology), University of Debrecen Egyetem [Debrecen], Plant Protection Department [Debrecen, Hungary] (Faculty of Agriculture and Food Sciences & Environmental Management), This work was supported by grants from the Austrian Science Foundation (FWF P-19143 and FWF P-19421) to CPK and BS, respectively. Work by SLC was supported by the Infrastructures en Biologie Santé et Agronomie (IBISA). TP is recipient of a Fondation Tuck Enerbio PhD. Fellowship. Work by LK, EF and ES was supported by the Hungarian Scientific Research Fund (OTKA, K67667) and the National Office for Research and Technology (NKTH, A2-2006-0017). EF is supported by a Bolyai János Research Scholarship (BO/00519/09/8)., Plateforme Génomique de l'IBENS, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), University of Debrecen, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Catabolite repression, Biológiai tudományok, Gene Knockout Techniques, MESH: Protein Structure, Tertiary, Természettudományok, Hypocrea, Transcription (biology), MESH: Up-Regulation, Trichoderma reesei, MESH: Gene Knockout Techniques, 2. Zero hunger, Genetics, 0303 health sciences, biology, Up-Regulation, Cell biology, MESH: Glucose, Phenotype, MESH: Repressor Proteins, Hypocreales, MESH: Genome, Fungal, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Fungal Proteins, Genome, Fungal, Research Article, Biotechnology, MESH: Mutation, lcsh:QH426-470, lcsh:Biotechnology, Repressor, MESH: Carbon, MESH: Hypocreales, MESH: Phenotype, Chromatin remodeling, Fungal Proteins, 03 medical and health sciences, Mediator, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene, 030304 developmental biology, Binding Sites, 030306 microbiology, biology.organism_classification, Carbon, Protein Structure, Tertiary, Repressor Proteins, lcsh:Genetics, Glucose, MESH: Binding Sites, Mutation
Abstract: Background The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known. Results Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus Trichoderma reesei (anamorph of Hypocrea jecorina) by profiling transcription in a wild-type and a delta-cre1 mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes. Conclusions Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.
Published: 2011

42. Yeast ancestral genome reconstructions: the possibilities of computational methods II

Author: Aïda Ouangraoua, Eric Tannier, Haris Gavranović, Cedric Chauve, Department of Mathematics [Burnaby] (SFU), Simon Fraser University (SFU.ca), UNIVERSITY OF SARAJEVO - UNIVERZITET U SARAJEVU, Bioinformatics and Sequence Analysis (BONSAI), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), 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 Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale pour la Recherche (grant ANR-08-GENM-036-01 ‘‘CoGeBi’’, Centre National de la Recherche Scientifique (CNRS), Ministère des Affaires étrangères et européennes (programmes ECO-NET et collaboration France-Canada), Natural Sciences and Engineering Research Council of Canada (NSERC), University of Sarajevo, UNIVERZITET U SARAJEVU, Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), 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)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-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)-École Centrale de Lyon (ECL), and Université de Lyon-Université Lumière - Lyon 2 (UL2)
Subjects: Genetic Markers, Most recent common ancestor, MESH: Gene Rearrangement, Molecular Sequence Data, Biology, MESH: Genetic Markers, algorithms, genomic rearrangements, Genome, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Gene Duplication, Gene orders, Genetics, Animals, MESH: Animals, MESH: Models, Genetic, MESH: Phylogeny, Molecular Biology, Phylogeny, MESH: Evolution, Molecular, 030304 developmental biology, Ancestor, Gene Rearrangement, 0303 health sciences, Sequence, MESH: Molecular Sequence Data, Models, Genetic, MESH: Gene Duplication, Chromosome Mapping, Computational Biology, computational molecular biology, Gene rearrangement, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Yeast, Computational Mathematics, Computational Theory and Mathematics, Evolutionary biology, Modeling and Simulation, combinatorics, MESH: Genome, Fungal, Genome, Fungal, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Chromosome Mapping, 030217 neurology & neurosurgery, MESH: Computational Biology
Abstract: International audience; Since the availability of assembled eukaryotic genomes, the first one being a budding yeast, many computational methods for the reconstruction of ancestral karyotypes and gene orders have been developed. The difficulty has always been to assess their reliability, since we often miss a good knowledge of the true ancestral genomes to compare their results to, as well as a good knowledge of the evolutionary mechanisms to test them on realistic simulated data. In this study, we propose some measures of reliability of several kinds of methods, and apply them to infer and analyse the architectures of two ancestral yeast genomes, based on the sequence of seven assembled extant ones. The pre-duplication common ancestor of S. cerevisiae and C. glabrata has been inferred manually by Gordon et al. (Plos Genet. 2009). We show why, in this case, a good convergence of the methods is explained by some properties of the data, and why results are reliable. In another study, Jean et al. (J. Comput Biol. 2009) proposed an ancestral architecture of the last common ancestor of S. kluyveri, K. thermotolerans, K. lactis, A. gossypii, and Z. rouxii inferred by a computational method. In this case, we show that the dataset does not seem to contain enough information to infer a reliable architecture, and we construct a higher resolution dataset which gives a good reliability on a new ancestral configuration.
Published: 2010

43. Dynamic evolution of megasatellites in yeasts

Author: Thomas Rolland, Bernard Dujon, Guy-Franck Richard, Université Pierre et Marie Curie - Paris 6 (UPMC), Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ministère de l’Enseignement Supérieur et de la Recherche [Doctoral fellowship to T.R.]. Funding for open access charge: 700000/024310, and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Pseudogene, Minisatellite Repeat, [SDV]Life Sciences [q-bio], Genes, Fungal, Candida glabrata, Saccharomyces cerevisiae, Biology, Evolution, Molecular, 03 medical and health sciences, Negative selection, 0302 clinical medicine, Tandem repeat, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene duplication, Genetics, MESH: Pseudogenes, Cluster Analysis, MESH: Candida glabrata, Gene, MESH: Evolution, Molecular, 030304 developmental biology, 0303 health sciences, Genomics, MESH: Cluster Analysis, MESH: Saccharomyces cerevisiae, MESH: Tandem Repeat Sequences, Minisatellite, Tandem Repeat Sequences, MESH: Genome, Fungal, Genome, Fungal, Homologous recombination, MESH: Genes, Fungal, 030217 neurology & neurosurgery, Pseudogenes
Abstract: International audience; Megasatellites are a new family of long tandem repeats, recently discovered in the yeast Candida glabrata. Compared to shorter tandem repeats, such as minisatellites, megasatellite motifs range in size from 135 to more than 300 bp, and allow calculation of evolutionary distances between individual motifs. Using divergence based on nucleotide substitutions among similar motifs, we determined the smallest distance between two motifs, allowing their subsequent clustering. Motifs belonging to the same cluster are recurrently found in different megasatellites located on different chromosomes, showing transfer of genetic information between megasatellites. In comparison, evolution of the few similar tandem repeats in Saccharomyces cerevisiae FLO genes mainly involves subtelomeric homologous recombination. We estimated selective constraints acting on megasatellite motifs and their host genes, and found that motifs are under strong purifying selection. Surprisingly, motifs inserted within pseudogenes are also under purifying selection, whereas the pseudogenes themselves evolve neutrally. We propose that megasatellite motifs propagate by a combination of three different molecular mechanisms: (i) gene duplication, (ii) ectopic homologous recombination and (iii) transfer of motifs from one megasatellite to another one. These mechanisms actively cooperate to create new megasatellites, that may play an important role in the adaptation of Candida glabrata to its human host.
Published: 2010

44. Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments

Author: Hugues Mathis, Antoine Margeot, AurÃ©lie Duclos, Laurent Jourdren, Thomas Portnoy, StÃ©phane Le Crom, Christian Brion, GenomiqueENS (Genomique ENS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Astrophysik (MPA), Max-Planck-Gesellschaft, IFP Energies nouvelles (IFPEN), Plateforme Génomique de l'IBENS, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: MESH: Oligonucleotide Probes, Biology, computer.software_genre, Multiplexing, 03 medical and health sciences, MESH: Software, Software, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Relevance (information retrieval), 030304 developmental biology, Oligonucleotide Array Sequence Analysis, Trichoderma, 0303 health sciences, Tiling array, business.industry, 030302 biochemistry & molecular biology, SIGNAL (programming language), Pipeline (software), MESH: Trichoderma, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Workflow, MESH: Genome, Fungal, MESH: Oligonucleotide Array Sequence Analysis, Methods Online, Data mining, DNA microarray, Genome, Fungal, business, Oligonucleotide Probes, computer
Abstract: International audience; Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/.
Published: 2010

45. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Author: Xiaohui Xie, Liande Li, B. Gillian Turgeon, Daren W. Brown, Christina A. Cuomo, Etienne Danchin, M. Carmen Ruiz-Roldán, Ilan Wapinski, Petra M. Houterman, Aviv Regev, Sharadha Sakthikumar, Diego Miranda-Saavedra, James E. Galagan, Lokesh Kumar, Michael Koehrsen, Divya Sain, Sean M. Sykes, Martijn Rep, Yong-Hwan Lee, Chinnappa D. Kodira, Andrew C. Diener, Li-Jun Ma, B. H. Bluhm, Won-Bo Shim, Kim E. Hammond-Kosack, H. Charlotte van der Does, Jeffrey J. Coleman, Jin-Rong Xu, David C. Schwartz, John F. Antoniw, John M. Manners, Robert H. Proctor, Sook Young Park, Sinéad B. Chapman, Seogchan Kang, Liane R. Gale, Kemal Kazan, Karen Hilburn, Pedro M. Coutinho, Olen C. Yoder, Stephen A. Goff, Robert A. E. Butchko, Gyungsoon Park, Bernard Henrissat, Katherine A. Borkovich, H. Corby Kistler, Michael Freitag, Aurélie Hua-Van, Mala Mukherjee, Scott E. Baker, Shiguo Zhou, Qiandong Zeng, Donald M. Gardiner, Manfred Grabherr, Wilfried Jonkers, Marie Josée Daboussi, Marie Dufresne, Andrew Breakspear, Charles P. Woloshuk, Antonio Di Pietro, Sarah Young, Richard M.R. Coulson, Jongsun Park, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], VU University Amsterdam, University of California [Riverside] (UCR), University of California, University of Arizona, Université Paris-Sud - Paris 11 (UP11), Universidad de Córdoba [Cordoba], Oregon State University (OSU), Architecture et fonction des Macromolécules Biologiques - UMR 6098 (AFMB), Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2, Pennsylvania State University (Penn State), Penn State System, Texas A&M University System, Purdue University, University of California [Irvine] (UCI), Rothamsted Research, Pacific Northwest National Laboratory (PNNL), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, USDA-ARS : Agricultural Research Service, European Molecular Biology Laboratory European Bioinformatics Institute, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), University of California [Davis] (UC Davis), ARS, Queensland Bioscience Precinct, Seoul National University [Seoul] (SNU), University of Cambridge [UK] (CAM), University of Wisconsin-Madison, Cornell University [New York], Independent, Molecular Plant Pathology (SILS, FNWI), Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Vrije Universiteit Amsterdam [Amsterdam] (VU), University of California [Riverside] (UC Riverside), University of California (UC), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Universidad de Córdoba = University of Córdoba [Córdoba], Purdue University [West Lafayette], University of California [Irvine] (UC Irvine), and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: MESH: Sequence Analysis, DNA, Proteome, MESH: Virulence, Genome, Fusarium, DISEASE RESISTANCE, MESH: Phylogeny, MAXIMUM-LIKELIHOOD, MESH: Evolution, Molecular, Phylogeny, Genomic organization, Genetics, MESH: Fusarium, 0303 health sciences, Multidisciplinary, biology, Virulence, MESH: Genomics, Fungal genetics, food and beverages, MESH: Synteny, Genomics, MESH: Chromosomes, Fungal, MESH: Proteome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Phenotype, Multigene Family, MESH: Genome, Fungal, Chromosomes, Fungal, Genome, Fungal, HOST PATHOGEN RELATIONSHIPS, FUSARIUM GRAMINEARUM, FUSARIUM VERTICILLIODES, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Plant disease resistance, MESH: Phenotype, MESH: Host-Parasite Interactions, Synteny, Article, Host-Parasite Interactions, Evolution, Molecular, 03 medical and health sciences, Fusarium oxysporum, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, FUSARIUM OXYSPORUM, 030304 developmental biology, RELATION HOTE-PARASITE, Comparative genomics, 030306 microbiology, Sequence Analysis, DNA, biology.organism_classification, POLYMORPHISM, MESH: Multigene Family, PATHOGENICITY
Abstract: International audience; Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
Published: 2010

46. Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus

Author: Dea Garcia-Hermoso, Gaël Lecellier, Odile Cabaret, Françoise Dromer, Martine Olivi, Cécile Farrugia, Stéphane Bretagne, Jean-Marc Costa, Laboratoire CERBA [Saint Ouen l'Aumône], Groupe Henri Mondor-Albert Chenevier, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Hôpital Albert Chenevier, Centre National de Référence des Mycoses invasives et antifongiques - Mycologie moléculaire (CNRMA), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), We thank the following principal investigators of the YEASTS Group who provided Candida albicans isolates. C. Bouges-Michel (hôpital Avicenne, Bobigny), I. Poilane (hôpital Jean Verdier, Bondy), J. Dunan (hôpital Ambroise Paré, Boulogne), G. Galeazzi (hôpital Louis Mourier, Colombes), F. Botterel (hôpital Henri Mondor, Créteil), N. Fauchet (Centre Intercommunal, Créteil), E. Forget (hôpital Beaujon, Clichy), C. Lawrence (hôpital Raymond Poincaré, Garches), C. Bonnal, F. Botterel, P. Bouree (hôpital du Kremlin Bicêtre, Kremlin-Bicêtre), O. Eloy (Centre Hospitalier, Le Chesnay), M.-F. David, N. Khassis, L. Milhaila (hôpital Paul Brousse, Villejuif), E. Chachaty (Institut Gustave Roussy, Villejuif), and in Paris: C. Chochillon (hôpital Bichat), A. Paugam, M.-T. Baixench (hôpital Cochin), M. Cornet (Hôtel Dieu), M.-C. Escande (Institut Curie), M.-E. Bougnoux, Y. Sterckers, S. Challier (hôpital Necker), E. Dannaoui, V. Lavarde (hôpital Européen Georges Pompidou), A. Datry, B. Lmimouni, S. Brun, A. Fekkar (hôpital de la Pitié-Salpétrière), J.-L. Poirot (hôpital Saint Antoine), C. Lacroix (hôpital Saint Louis), D. Moissenet (hôpital Trousseau), M. Develoux (hôpital Tenon), S. Bonacorsi (hôpital Robert Debré)., Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Hôpital Albert Chenevier, Laboratoire de génétique et biologie cellulaire (LGBC), Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie
Subjects: Microbiology (medical), Genotyping, MESH: Sequence Analysis, DNA, Locus (genetics), MESH: Nucleic Acid Denaturation, Biology, Nucleic Acid Denaturation, Polymerase Chain Reaction, Microbiology, High Resolution Melt, 03 medical and health sciences, High-resolution melting, Tandem repeat, Genotype, Candida albicans, MESH: Polymorphism, Genetic, Humans, Typing, MESH: Genetic Variation, DNA, Fungal, Molecular Biology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, Genetics, Single-nucleotide polymorphism, 0303 health sciences, Polymorphism, Genetic, MESH: Humans, 030306 microbiology, MESH: Candida albicans, Candidiasis, Genetic Variation, MESH: Polymerase Chain Reaction, Sequence Analysis, DNA, MESH: Candidiasis, MESH: DNA, Fungal, Genetic marker, MESH: Genome, Fungal, Microsatellite, MESH: Microsatellite Repeats, Genome, Fungal, Microsatellite length polymorphism, Microsatellite Repeats
Abstract: International audience; Microsatellite length polymorphism (MLP) typing is a PCR-based method used for genotyping of the diploid yeast Candida albicans. However, MLP is subject to homoplasia which can hamper the accuracy of the results. We combined fragment length analysis, high-resolution DNA melting (HRM) analysis, and SNaPshot minisequencing after a single amplification of the CDC3 locus to study 95 epidemiologically independent C. albicans isolates. HRM analysis for a given electrophoretic group led to a maximum of three different curves due to the presence of a SNP upstream of the tandem repeat which could be characterized using the SNaPshot assay. The combination of the three methods had a discriminatory index of 0.88 in complete congruence with previous MLP typing (Mantel test R=0.99, P
Published: 2010

47. FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology

Author: Olivier Lespinet, Sandrine Grossetete, Bernard Labedan, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Databases, Protein, MESH: Fungi, lcsh:QH426-470, lcsh:Biotechnology, Biology, Proteomics, Genome, Database, 03 medical and health sciences, lcsh:TP248.13-248.65, Genetics, Data Mining, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Databases, Protein, Gene, 030304 developmental biology, 0303 health sciences, MESH: Data Mining, 030302 biochemistry & molecular biology, Fungi, Computational Biology, 15. Life on land, Metabolic pathway, lcsh:Genetics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Functional annotation, MESH: Metabolic Networks and Pathways, MESH: Genome, Fungal, Genome, Fungal, DNA microarray, Metabolic Networks and Pathways, MESH: Computational Biology, Biotechnology
Abstract: Background More and more completely sequenced fungal genomes are becoming available and many more sequencing projects are in progress. This deluge of data should improve our knowledge of the various primary and secondary metabolisms of Fungi, including their synthesis of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional annotation of many fungal genomes is imperfect, especially of genes encoding enzymes, so we need dedicated tools to analyze their metabolic pathways in depth. Description FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances. It is freely accessible at http://www.fungipath.u-psud.fr. Conclusions As more and more fungal genomes are expected to be sequenced during the coming years, FUNGIpath should help progressively to reconstruct the ancestral primary and secondary metabolisms of the main branches of the fungal tree of life and to elucidate the evolution of these ancestral fungal metabolisms to various specific derived metabolisms.
Published: 2010

48. Comparative transcript profiling of Candida albicans and Candida dubliniensis identifies SFL2, a C. albicans gene required for virulence in a reconstituted epithelial infection model

Author: Judy Higgins, Murielle Chauvel, Donna M. MacCallum, Gary P. Moran, Derek J. Sullivan, Tim Yeomans, David C. Coleman, Karsten Hokamp, Martin J. Spiering, Christophe d'Enfert, Division of Oral Biosciences, Trinity College Dublin, Biologie et Pathogénicité fongiques, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], University of Aberdeen, Genetics, This work was supported by a grant from Science Foundation Ireland (Programme Investigator grant no. 04/IN3/B463) to D. Sullivan and grants from the European Commission to C. d'Enfert. (Galar Fungail 2 Marie Curie Research Training Network, MRTN-CT-2003-504148, FINSysB Marie Curie Initial Training Network, PITN-GA-2008-214004)., European Project: 214004,PEOPLE,FP7-PEOPLE-2007-1-1-ITN,FINSYSB(2008), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA)
Subjects: Transcription, Genetic, MESH: Virulence, Mice, Gene Expression Regulation, Fungal, Candida albicans, Gene expression, MESH: Animals, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Candida, Mice, Inbred BALB C, 0303 health sciences, Fungal protein, Virulence, biology, Candidiasis, Articles, General Medicine, Corpus albicans, MESH: Candidiasis, MESH: Models, Animal, MESH: Epithelial Cells, Models, Animal, MESH: Genome, Fungal, Female, MESH: Fungal Proteins, Genome, Fungal, Candida dubliniensis, MESH: Gene Expression Regulation, Fungal, Genes, Fungal, MESH: Mice, Inbred BALB C, Microbiology, Fungal Proteins, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: Candida, Animals, Molecular Biology, Gene, MESH: Mice, 030304 developmental biology, 030306 microbiology, Gene Expression Profiling, MESH: Transcription, Genetic, MESH: Candida albicans, Epithelial Cells, biology.organism_classification, Gene expression profiling, MESH: Genes, Fungal, MESH: Female
Abstract: Candida albicans and Candida dubliniensis are closely related species displaying differences in virulence and genome content, therefore providing potential opportunities to identify novel C. albicans virulence genes. C. albicans gene arrays were used for comparative analysis of global gene expression in the two species in reconstituted human oral epithelium (RHE). C. albicans (SC5314) showed upregulation of hypha-specific and virulence genes within 30 min postinoculation, coinciding with rapid induction of filamentation and increased RHE damage. C. dubliniensis (CD36) showed no detectable upregulation of hypha-specific genes, grew as yeast, and caused limited RHE damage. Several genes absent or highly divergent in C. dubliniensis were upregulated in C. albicans . One such gene, SFL2 ( orf19.3969 ), encoding a putative heat shock factor, was deleted in C. albicans . ΔΔ sfl2 cells failed to filament under a range of hypha-inducing conditions and exhibited greatly reduced RHE damage, reversed by reintroduction of SFL2 into the ΔΔ sfl2 strain. Moreover, SFL2 overexpression in C. albicans triggered hyphal morphogenesis. Although SFL2 deletion had no apparent effect on host survival in the murine model of systemic infection, ΔΔ sfl2 strain-infected kidney tissues contained only yeast cells. These results suggest a role for SFL2 in morphogenesis and an indirect role in C. albicans pathogenesis in epithelial tissues.
Published: 2009

49. Gene Responses to Oxygen Availability in Kluyveromyces lactis: an Insight on the Evolution of the Oxygen-Responding System in Yeast

Author: Monique Bolotin-Fukuhara, Wei-Guo Bao, Ai-Lian Chen, Guanghui Wang, You-Fang Li, Yu-Yang Li, Jianping Liu, Zi-An Fang, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Sequence Homology, Amino Acid, lcsh:Medicine, MESH: Amino Acid Sequence, MESH: Base Sequence, Genome, Saccharomyces, MESH: Kluyveromyces, Kluyveromyces, Gene Expression Regulation, Fungal, Cloning, Molecular, lcsh:Science, Genetics, Kluyveromyces lactis, 0303 health sciences, Multidisciplinary, Microbiology/Microbial Evolution and Genomics, MESH: Genomics, 030302 biochemistry & molecular biology, Genomics, MESH: Saccharomyces cerevisiae, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Stochastic Processes, MESH: Genome, Fungal, Microbiology/Microbial Physiology and Metabolism, Genome, Fungal, MESH: Oxygen, MESH: Gene Expression Regulation, Fungal, MESH: Computational Biology, Research Article, Genome evolution, Saccharomyces cerevisiae, Molecular Sequence Data, Biology, Models, Biological, 03 medical and health sciences, MESH: Cloning, Molecular, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Gene, 030304 developmental biology, Stochastic Processes, MESH: Molecular Sequence Data, Base Sequence, Sequence Homology, Amino Acid, lcsh:R, MESH: Models, Biological, Computational Biology, Genetics and Genomics, biology.organism_classification, Oxygen, Schizosaccharomyces pombe, lcsh:Q
Abstract: International audience; The whole-genome duplication (WGD) may provide a basis for the emergence of the very characteristic life style of Saccharomyces cerevisiae-its fermentation-oriented physiology and its capacity of growing in anaerobiosis. Indeed, we found an over-representation of oxygen-responding genes in the ohnologs of S. cerevisiae. Many of these duplicated genes are present as aerobic/hypoxic(anaerobic) pairs and form a specialized system responding to changing oxygen availability. HYP2/ANB1 and COX5A/COX5B are such gene pairs, and their unique orthologs in the 'non-WGD' Kluyveromyces lactis genome behaved like the aerobic versions of S. cerevisiae. ROX1 encodes a major oxygen-responding regulator in S. cerevisiae. The synteny, structural features and molecular function of putative KlROX1 were shown to be different from that of ROX1. The transition from the K. lactis-type ROX1 to the S. cerevisiae-type ROX1 could link up with the development of anaerobes in the yeast evolution. Bioinformatics and stochastic analyses of the Rox1p-binding site (YYYATTGTTCTC) in the upstream sequences of the S. cerevisiae Rox1p-mediated genes and of the K. lactis orthologs also indicated that K. lactis lacks the specific gene system responding to oxygen limiting environment, which is present in the 'post-WGD' genome of S. cerevisiae. These data suggested that the oxygen-responding system was born for the specialized physiology of S. cerevisiae.
Published: 2009

50. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing

Author: Irina S. Druzhinina, Bernhard Seiboth, Randy M. Berka, Len A. Pennacchio, Antoine Margeot, David E. Culley, Hugues Mathis, Joel Martin, Frédéric Monot, Scott E. Baker, Jon K. Magnuson, Michael Rey, James R. Collett, Stéphane Le Crom, Barbara Cherry, Wendy Schackwitz, Christian P. Kubicek, Plateforme Génomique de l'IBENS, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique moléculaire du développement, Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-IFR36-Institut National de la Santé et de la Recherche Médicale (INSERM), US Department of Energy Joint Genome Institute, University of California, US Department of Energy Joint BioEnergy Institute, Research Area Biotechnology and Microbiology, Vienna University of Technology (TU Wien)-Institute of Chemical Engineering, Max-Planck-Institut für Astrophysik (MPA), Max-Planck-Gesellschaft, IFP Energies nouvelles (IFPEN), Vienna University of Technology (TU Wien), Groupe de spectrométrie moléculaire et atmosphérique (GSMA), Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), Novozymes, Inc., Partenaires INRAE, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: MESH: Sequence Analysis, DNA, MESH: Mutation, Genes, Fungal, Cellulase, Biology, Polymorphism, Single Nucleotide, 7. Clean energy, DNA sequencing, Microbiology, Fungal Proteins, 03 medical and health sciences, MESH: Base Composition, Species Specificity, Hypocrea, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Species Specificity, DNA, Fungal, Gene, Trichoderma reesei, 030304 developmental biology, Trichoderma, 2. Zero hunger, Genetics, Base Composition, 0303 health sciences, Fungal protein, Multidisciplinary, Massive parallel sequencing, 030306 microbiology, MESH: Polymorphism, Single Nucleotide, MESH: Cellulase, Sequence Analysis, DNA, Biological Sciences, biology.organism_classification, MESH: Trichoderma, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: DNA, Fungal, genomic DNA, Mutation, MESH: Genome, Fungal, biology.protein, MESH: Fungal Proteins, Genome, Fungal, MESH: Genes, Fungal
Abstract: Trichoderma reesei (teleomorph Hypocrea jecorina ) is the main industrial source of cellulases and hemicellulases harnessed for the hydrolysis of biomass to simple sugars, which can then be converted to biofuels such as ethanol and other chemicals. The highly productive strains in use today were generated by classical mutagenesis. To learn how cellulase production was improved by these techniques, we performed massively parallel sequencing to identify mutations in the genomes of two hyperproducing strains (NG14, and its direct improved descendant, RUT C30). We detected a surprisingly high number of mutagenic events: 223 single nucleotides variants, 15 small deletions or insertions, and 18 larger deletions, leading to the loss of more than 100 kb of genomic DNA. From these events, we report previously undocumented non-synonymous mutations in 43 genes that are mainly involved in nuclear transport, mRNA stability, transcription, secretion/vacuolar targeting, and metabolism. This homogeneity of functional categories suggests that multiple changes are necessary to improve cellulase production and not simply a few clear-cut mutagenic events. Phenotype microarrays show that some of these mutations result in strong changes in the carbon assimilation pattern of the two mutants with respect to the wild-type strain QM6a. Our analysis provides genome-wide insights into the changes induced by classical mutagenesis in a filamentous fungus and suggests areas for the generation of enhanced T. reesei strains for industrial applications such as biofuel production.
Published: 2009

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