Journal
BMC GENOMICS
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12864-015-1252-7
Keywords
Genome sequence; Conjugative transposon; Integrative and conjugative element; Single-molecule real-time sequencing
Funding
- Veni and a Vidi fellowship from the Netherlands Organization for Scientific Research
- Gisela Thier Fellowship from the Leiden University Medical Center
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Background: Clostridium difficile strain 630 Delta erm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns. Results: In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain. Conclusions: Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.
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