title: Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles.
abstract: Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. - Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes.
  
  
  
  The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin.
  
  
  
  The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles.
authors.affiliation: Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zürich, 8092, Zürich, Switzerland.
authors.forename: Markus
authors.initials: M
authors.lastname: Schlegel
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Münsterkötter
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.|Department of Genome-oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354, Freising, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Güldener
authors.affiliation: Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Berne, Baltzerstrasse 6, 3012, Bern, Switzerland.
authors.forename: Rémy
authors.initials: R
authors.lastname: Bruggmann
authors.affiliation: Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zürich, 8092, Zürich, Switzerland.
authors.forename: Angelo
authors.initials: A
authors.lastname: Duò
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Hainaut
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.|DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
authors.forename: Christian M K
authors.initials: CM
authors.lastname: Sieber
authors.affiliation: Friedrich-Schiller-Universität, Pharmazeutische Mikrobiologie, Winzerlaer Strasse 2, 07745, Jena, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Hoffmeister
authors.affiliation: Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zürich, 8092, Zürich, Switzerland. christoph.gruenig@microsynth.ch.|Microsynth AG, Schützenstrasse 15, 9436, Balgach, Switzerland. christoph.gruenig@microsynth.ch.
authors.forename: Christoph R
authors.initials: CR
authors.lastname: Grünig
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D060026:Endophytes / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D063990:Gene Ontology; D022761:Gene Transfer, Horizontal; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D005810:Multigene Family; D018517:Plant Roots / Q000382:microbiology*; D034622:RNA Interference; D012091:Repetitive Sequences, Nucleic Acid; D064210:Secondary Metabolism / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements
keywords: Comparative genomics; Lifestyle; Parasitism-mutualism continuum; Root endophyte; Species complex