title: Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses.
abstract: The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts.
  
  
  
  The genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type.
  
  
  
  Both cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Penselin
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Münsterkötter
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Kirsten
authors.affiliation: Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Felder
authors.affiliation: Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.affiliation: Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.affiliation: Institute of Medical Genetics, Cardiff University, Cardiff, UK.
authors.forename: Kevin
authors.initials: K
authors.lastname: Ashelford
authors.affiliation: Exeter Sequencing Service, Biosciences, University of Exeter, Exeter, UK.
authors.forename: Konrad H
authors.initials: KH
authors.lastname: Paskiewicz
authors.affiliation: NIAB EMR, East Malling, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Harrison
authors.affiliation: Applied Bioinformatics, Rothamsted Research, Harpenden, Hertfordshire, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Hughes
authors.affiliation: Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wolf
authors.affiliation: Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Shelest
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany.
authors.forename: Jenny
authors.initials: J
authors.lastname: Graap
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Hoffmann
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany.|Present address: Food Quality and Nutrition, Agroscope, Bern, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Wenzel
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Wöltje
authors.affiliation: Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: King
authors.affiliation: Biological and Environmental Sciences, University of Hertfordshire, Hatfield, Hertfordshire, UK.
authors.forename: Bruce D L
authors.initials: BD
authors.lastname: Fitt
authors.affiliation: Department of Genome-Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Güldener
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland.
authors.forename: Anna
authors.initials: A
authors.lastname: Avrova
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany. wknogge@ipb-halle.de.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Knogge
mesh_terms: D000595:Amino Acid Sequence; D001203:Ascomycota / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D021901:DNA, Intergenic; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D058507:Host Specificity; D005810:Multigene Family; D010802:Phylogeny; D006109:Poaceae / Q000382:microbiology*; D064210:Secondary Metabolism / Q000235:genetics
chemical_list: D021901:DNA, Intergenic
keywords: CAZymes; Effectors; Host specificity; Leotiomycetes; Non-ribosomal peptide synthetases; Phylogenetic evolution; Polyketide synthases; Rhynchosporium; Sex-related genes; Whole genome sequencing