title: Functional annotation of the Ophiostoma novo-ulmi genome: insights into the phytopathogenicity of the fungal agent of Dutch elm disease.
abstract: The ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years. We proceeded to annotate the genome of the O. novo-ulmi strain H327 that was sequenced in 2012. The 31.784-Mb nuclear genome (50.1% GC) is organized into 8 chromosomes containing a total of 8,640 protein-coding genes that we validated with RNA sequencing analysis. Approximately 53% of these genes have their closest match to Grosmannia clavigera kw1407, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (5%) orphans. A relatively small portion (∼3.4%) of the genome is occupied by repeat sequences; however, the mechanism of repeat-induced point mutation appears active in this genome. Approximately 76% of the proteins could be assigned functions using Gene Ontology analysis; we identified 311 carbohydrate-active enzymes, 48 cytochrome P450s, and 1,731 proteins potentially involved in pathogen-host interaction, along with 7 clusters of fungal secondary metabolites. Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted. Our analysis identified a specific genetic arsenal impacting the sexual and vegetative growth, phytopathogenicity, and signaling/plant-defense-degradation relationship between O. novo-ulmi and its elm host and insect vectors.
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada Present address: Department of Pharmacology, Dalhousie University, Halifax, NS, Canada.
authors.forename: André M
authors.initials: AM
authors.lastname: Comeau
authors.affiliation: Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada.
authors.forename: Josée
authors.initials: J
authors.lastname: Dufour
authors.affiliation: Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada.
authors.forename: Guillaume F
authors.initials: GF
authors.lastname: Bouvet
authors.affiliation: Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada.
authors.forename: Volker
authors.initials: V
authors.lastname: Jacobi
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada.
authors.forename: Martha
authors.initials: M
authors.lastname: Nigg
authors.affiliation: Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Laroche
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada.
authors.forename: Roger C
authors.initials: RC
authors.lastname: Levesque
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada louis.bernier@sbf.ulaval.ca.
authors.forename: Louis
authors.initials: L
authors.lastname: Bernier
mesh_terms: D001482:Base Composition / Q000235:genetics; D015825:Chromosomes, Fungal / Q000235:genetics; D049770:Genes, Mating Type, Fungal; D016681:Genome, Fungal; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D055156:Ophiostoma / Q000235:genetics* / Q000472:pathogenicity*; D010935:Plant Diseases / Q000382:microbiology*; D018626:Retroelements / Q000235:genetics; D016615:Telomere / Q000235:genetics; D034403:Ulmus / Q000382:microbiology*
chemical_list: D018626:Retroelements
keywords: CAZyme; cytochrome P450; mating-type; phytopathogen; terpene degradation