title: The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum.
abstract: BACKGROUND
  Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.
  
  
  RESULTS
  We have comprehensively completed the genomic 36,563,796 bp sequence by replacing unknown bases, placing supercontigs within their correct loci, correcting assembly errors, and inserting new sequences which include for the first time complete AT rich sequences such as centromere sequences, subtelomeric regions and the telomeres. Each of the four F. graminearium chromosomes was found to be submetacentric with respect to centromere positioning. The position of a potential neocentromere was also defined. A preferentially higher frequency of genetic recombination was observed at the end of the longer arm of each chromosome. Within the genome 1529 gene models have been modified and 412 new gene models predicted, with a total gene call of 14,164. The re-annotation impacts upon 69 entries held within the Pathogen-Host Interactions database (PHI-base) which stores information on genes for which mutant phenotypes in pathogen-host interactions have been experimentally tested, of which 59 are putative transcription factors, 8 kinases, 1 ATP citrate lyase (ACL1), and 1 syntaxin-like SNARE gene (GzSYN1). Although the completed F. graminearum contains very few transposon sequences, a previously unrecognised and potentially active gypsy-type long-terminal-repeat (LTR) retrotransposon was identified. In addition, each of the sub-telomeres and centromeres contained either a LTR or MarCry-1_FO element. The full content of the proposed ancient chromosome fusion sites has also been revealed and investigated. Regions with high recombination previously noted to be rich in secretome encoding genes were also found to be rich in tRNA sequences. This study has identified 741 F. graminearum species specific genes and provides the first complete genome assembly for a Sordariomycetes species.
  
  
  CONCLUSIONS
  This fully completed F. graminearum PH-1 genome and manually curated annotation, available at Ensembl Fungi, provides the optimum resource to perform interspecies comparative analyses and gene function studies.
authors.affiliation: Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK. robert.king@rothamsted.ac.uk.
authors.forename: Robert
authors.initials: R
authors.lastname: King
authors.affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK. martin.urban@rothamsted.ac.uk.
authors.forename: Martin
authors.initials: M
authors.lastname: Urban
authors.affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK. michael.hammond-kosack@rothamsted.ac.uk.
authors.forename: Michael C U
authors.initials: MC
authors.lastname: Hammond-Kosack
authors.affiliation: Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK. keywan.hassani-pak@rothamsted.ac.uk.
authors.forename: Keywan
authors.initials: K
authors.lastname: Hassani-Pak
authors.affiliation: Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK. kim.hammond-kosack@rothamsted.ac.uk.
authors.forename: Kim E
authors.initials: KE
authors.lastname: Hammond-Kosack
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D005670:Fusarium / Q000235:genetics* / Q000472:pathogenicity; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D017422:Sequence Analysis, DNA