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Manual curation and reannotation of the genomes of Clostridium difficile 630Δerm and C. difficile 630
Henning Dannheim1, Thomas Riedel2, Meina Neumann-Schaal1
1Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany.
Purpose:
We resequenced the genome of Clostridium difficile 630Δerm (DSM 28645), a model strain commonly used for the generation of insertion mutants.
Methodology:
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.
Conclusion:
Based on the genomic analysis, several new metabolic features of C. difficile are proposed and could be supported by literature and subsequent experiments.