title: Manual curation and reannotation of the genomes of Clostridium difficile 630Δerm and C. difficile 630.
abstract: OBJECTIVE
  We resequenced the genome of Clostridium difficile 630Δerm (DSM 28645), a model strain commonly used for the generation of insertion mutants.
  
  
  METHODS
  The genome sequence was obtained by a combination of single-molecule real-timeand Illumina sequencing technology.
  
  
  RESULTS
  Detailed manual curation and comparison to the previously published genomic sequence revealed sequence differences including inverted regions and the presence of plasmid pCD630. Manual curation of our previously deposited genome sequence of the parental strain 630 (DSM 27543) led to an improved genome sequence. In addition, the sequence of the transposon Tn5397 was completely identified. We manually revised the current manual annotation of the initial sequence of strain 630 and modified either gene names, gene product names or assigned EC numbers of 57 % of genes. The number of hypothetical and conserved hypothetical proteins was reduced by 152. This annotation was used as a template to annotate the most recent genome sequences of the strains 630Δerm and 630.
  
  
  CONCLUSIONS
  Based on the genomic analysis, several new metabolic features of C. difficile are proposed and could be supported by literature and subsequent experiments.
authors.affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany.
authors.forename: Henning
authors.initials: H
authors.lastname: Dannheim
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Riedel
authors.affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany.
authors.forename: Meina
authors.initials: M
authors.lastname: Neumann-Schaal
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.|German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Boyke
authors.initials: B
authors.lastname: Bunk
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Isabel
authors.initials: I
authors.lastname: Schober
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.|German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Cathrin
authors.initials: C
authors.lastname: Spröer
authors.affiliation: Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany.
authors.forename: Cynthia Maria
authors.initials: CM
authors.lastname: Chibani
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.|German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Gronow
authors.affiliation: Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany.
authors.forename: Heiko
authors.initials: H
authors.lastname: Liesegang
authors.affiliation: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.|German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Overmann
authors.affiliation: Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany.
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
mesh_terms: D001483:Base Sequence; D001647:Bile Acids and Salts; D016360:Clostridioides difficile / Q000235:genetics* / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics; D008401:Gas Chromatography-Mass Spectrometry; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D016366:Open Reading Frames; D018384:Oxidative Stress / Q000235:genetics; D020641:Polymorphism, Single Nucleotide
chemical_list: D001647:Bile Acids and Salts; D004269:DNA, Bacterial