Manual curation and reannotation of the genomes of Clostridium difficile 630 Delta erm and C. difficile 630

作者：Dannheim Henning; Riedel Thomas; Neumann Schaal Meina; Bunk Boyke; Schober Isabel; Sproeer Cathrin; Chibani Cynthia Maria; Gronow Sabine; Liesegang Heiko; Overmann Joerg; Schomburg Dietmar

来源：Journal of Medical Microbiology, 2017, 66(3): 286-293.

DOI：10.1099/jmm.0.000427

• Clostridium difficile
• annotation
• genome
• Stickland reaction
• bile acids
• oxidative stress

Purpose. We resequenced the genome of Clostridium difficile 630 Delta erm (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 630 Delta erm 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.

• 出版日期2017-3