title: The genome of the emerging barley pathogen Ramularia collo-cygni.
abstract: Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality.
  
  
  
  The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified.
  
  
  
  The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph.
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK. graham.mcgrann@sruc.ac.uk.
authors: Graham R D
authors: GR
authors: McGrann
authors: Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
authors: Ambrose
authors: A
authors: Andongabo
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.|Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3TF, UK.
authors: Elisabet
authors: E
authors: Sjökvist
authors: Edinburgh Genomics, The University of Edinburgh, Edinburgh, EH9 3JT, UK.
authors: Urmi
authors: U
authors: Trivedi
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Francois
authors: F
authors: Dussart
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.|Present address: Forest Research, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, UK.
authors: Maciej
authors: M
authors: Kaczmarek
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Ashleigh
authors: A
authors: Mackenzie
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.|Present address: Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
authors: James M
authors: JM
authors: Fountaine
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Jeanette M G
authors: JM
authors: Taylor
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Linda J
authors: LJ
authors: Paterson
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Kalina
authors: K
authors: Gorniak
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Fiona
authors: F
authors: Burnett
authors: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
authors: Kostya
authors: K
authors: Kanyuka
authors: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
authors: Kim E
authors: KE
authors: Hammond-Kosack
authors: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
authors: Jason J
authors: JJ
authors: Rudd
authors: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3TF, UK.|Edinburgh Genomics, The University of Edinburgh, Edinburgh, EH9 3JT, UK.
authors: Mark
authors: M
authors: Blaxter
authors: Crop Protection Team, Crop and Soil Systems Group, SRUC, West Mains Road, Edinburgh, EH9 3JG, UK.
authors: Neil D
authors: ND
authors: Havis
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D005656:Fungal Proteins; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D001467:Hordeum / Q000382:microbiology*; D058977:Molecular Sequence Annotation; D010641:Phenotype; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D018515:Plant Leaves / Q000382:microbiology; D020543:Proteome; D040901:Proteomics / Q000379:methods; D064210:Secondary Metabolism; D014774:Virulence / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D020543:Proteome
keywords: Dothideomycetes; Endophyte; Necrotroph; Ramularia leaf spot; Rubellin toxin; Whole genome sequencing