title: Sequencing and annotation of the Ophiostoma ulmi genome.
abstract: BACKGROUND
  The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics.
  
  
  RESULTS
  We have sequenced the 31.5 Mb genome of O.ulmi using Illumina next generation sequencing. Applying both de novo and comparative genome annotation methods, we predict a total of 8639 gene models. The quality of the predicted genes was validated using a variety of data sources consisting of EST data, mRNA-seq data and orthologs from related fungal species. Sequence-based computational methods were used to identify candidate virulence-related genes. Metabolic pathways were reconstructed and highlight specific enzymes that may play a role in virulence.
  
  
  CONCLUSIONS
  This genome sequence will be a useful resource for further research aimed at understanding the molecular mechanisms of pathogenicity by O. ulmi. It will also facilitate the identification of enzymes necessary for industrial biotransformation applications.
authors.affiliation: Department of Cell & Systems Biology University of Toronto, Toronto, Canada.
authors.forename: Shima
authors.initials: S
authors.lastname: Khoshraftar
authors.forename: Stacy
authors.initials: S
authors.lastname: Hung
authors.forename: Sadia
authors.initials: S
authors.lastname: Khan
authors.forename: Yunchen
authors.initials: Y
authors.lastname: Gong
authors.forename: Vibha
authors.initials: V
authors.lastname: Tyagi
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
authors.forename: Mohini
authors.initials: M
authors.lastname: Sain
authors.forename: Alan M
authors.initials: AM
authors.lastname: Moses
authors.forename: Dinesh
authors.initials: D
authors.lastname: Christendat
mesh_terms: D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D055156:Ophiostoma / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D014774:Virulence / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D012333:RNA, Messenger