Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
2011
Amselem, Joelle, J. | Cuomo, Christina A. | van Kan, Jan A. L. | Viaud, Muriel | Benito, Ernesto P. | Couloux, Arnaud | Coutinho, Pedro, M | de Vries, Ronald P. | Dyer, Paul S. | Fillinger-David, Sabine, Helma | Fournier, Elisabeth | Gout, Lilian | Hahn, Matthias | Kohn, Linda | Lapalu, Nicolas | Plummer, Kim M. | Pradier, Jean-Marc | Quevillon, Emmanuel | Sharon, Amir | Simon, Adeline | ten Have, Arjen | Tudzynski, Bettina | Tudzynski, Paul | Wincker, Patrick | Andrew, Marion | Anthouard, Véronique | Beever, Ross E. | Beffa, Rolland | Benoit, Isabelle | Bouzid, Ourdia | Brault, Baptiste | Chen, Zehua | Choquer, Mathias | Collemare, Jerome | Cotton, Pascale | Danchin, Etienne | da Silva, Corinne | Gautier, Angelique | Giraud-Delville, Corinne | Giraud, Tatiana | Gonzalez, Celedonio | Grossetete, Sandrine | Gueldener, Ulrich | Henrissat, Bernard | Howlett, Barbara J. | Kodira, Chinnappa | Kretschmer, Matthias | Lappartient, Anne | Leroch, Michaela | Levis, Caroline | Mauceli, Evan | Neuvéglise, Cécile | Oeser, Birgitt | Pearson, Matthew | Poulain, Julie | Poussereau, Nathalie | Quesneville, Hadi | Rascle, Christine | Schumacher, Julia | Segurens, Béatrice | Sexton, Adrienne | Silva, Evelyn | Sirven, Catherine | Soanes, Darren M. | Talbot, Nicholas J. | Templeton, Matt | Yandava, Chandri | Yarden, Oded | Zeng, Qiandong | Rollins, Jeffrey A. | Lebrun, Marc-Henri | Dickman, Marty | Unité de Recherche Génomique Info (URGI) ; Institut National de la Recherche Agronomique (INRA) | BIOlogie et GEstion des Risques en agriculture (BIOGER) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Broad Institute of MIT and Harvard (BROAD INSTITUTE) ; Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston] | Wageningen University and Research [Wageningen] (WUR) | Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias ; Universidad de Salamanca [España] = University of Salamanca [Spain] | Genoscope - Centre national de séquençage [Evry] (GENOSCOPE) ; Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) | Architecture et fonction des macromolécules biologiques (AFMB) ; Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) | Kluyver Centre for Genomics of Industrial Fermentations | Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre (CBS-KNAW) | School of Biology ; University of Nottingham, UK (UON) | Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Faculty of Biology ; University of Kaiserslautern | Biology Department ; University of Toronto | Botany Department ; La Trobe University [Melbourne] | Microbiologie, adaptation et pathogénie (MAP) ; Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) ; Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS) | Department of Molecular Microbiology and Biotechnology ; Tel Aviv University (TAU) | Instituto de Investigaciones Biológicas [Mar del Plata] (IIB) ; Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas y Naturales [Mar del Plata] ; Universidad Nacional de Mar del Plata [Mar del Plata] (UNMdP)-Universidad Nacional de Mar del Plata [Mar del Plata] (UNMdP) | Molekularbiologie und Biotechnologie der Pilze ; Institut für Biologie und Biotechnologie der Pflanzen ; Westfälische Wilhelms-Universität Münster = University of Münster (WWU)-Westfälische Wilhelms-Universität Münster = University of Münster (WWU) | Manaaki Whenua – Landcare Research [Lincoln] | Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath) ; Microbiologie, adaptation et pathogénie (MAP) ; Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) ; Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-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) | Laboratory of Phytopathology ; Wageningen University and Research [Wageningen] (WUR) | Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes ; Centre National de la Recherche Scientifique (CNRS) | Interactions Biotiques et Santé Végétale (IBSV) ; Institut National de la Recherche Agronomique (INRA) | Ecologie Systématique et Evolution (ESE) ; Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS) | Departamento de Bioquímica y Biología Molecular ; Universidad de La Laguna [Tenerife - SP] (ULL) | Helmholtz Zentrum München = German Research Center for Environmental Health (HMGU) | School of Botany [Melbourne] ; Faculty of Science [Melbourne] ; University of Melbourne-University of Melbourne | MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Centre National de la Recherche Scientifique (CNRS) | Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas ; Universidad Andrés Bello [Santiago] (UNAB) | School of Biosciences ; University of Exeter | Plant and Food Research ; Mt. Albert Research Centre | Department of Plant Pathology and Microbiology ; The Hebrew University of Jerusalem (HUJ) | Department of Plant Pathology ; University of Florida [Gainesville] (UF) | Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology ; Institute for Plant Genomics and Biotechnology | ANR-07-BIOE-0006,E-TRICEL,Exploration de la biodiversité enzymatique pour la complémentation du secrétome de Trichoderma reesei afin d'améliorer l'hydrolyse des lignocelluloses(2007) | European Project: LSHB-CT-2004-511952
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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