Henning Dannheim1, Thomas Riedel2, Meina Neumann-Schaal1, Boyke Bunk2,3, Isabel Schober2, Cathrin Spröer2,3, Cynthia Maria Chibani4, Sabine Gronow2,3, Heiko Liesegang4, Jörg Overmann2,3, Dietmar Schomburg1. 1. Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig and Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany. 2. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany. 3. German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany. 4. Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany.
Abstract
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.
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.
Authors: Matthias Steglich; Julia D Hofmann; Julia Helmecke; Johannes Sikorski; Cathrin Spröer; Thomas Riedel; Boyke Bunk; Jörg Overmann; Meina Neumann-Schaal; Ulrich Nübel Journal: Front Microbiol Date: 2018-05-08 Impact factor: 5.640