6/SCS2.8 to obtain FASTQ-formatted sequence data. De novo assembly of short DNA reads and gap-closing The 80-mer reads were assembled (parameters k64, n51, c32.1373) using ABySS-pe v1.2.0 [32]. Predicted gaps were amplified with a specific PCR primer pair, followed by
Sanger DNA sequencing using a BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA). Validation of the complete genome sequence using short-read mapping and pulsed-field gel electrophoresis (PFGE) To validate the genome sequence, 40–mer short reads were re-aligned with the sequence using Maq software (ver. 0.7.1) and the easyrun Perl-command [33]. Read alignment was inspected using the MapView graphical alignment viewer [34]. PFGE find more analysis was performed to validate the predicted restriction fragment profiles from the complete genome sequence, according to De Zoysa CAL-101 price I-BET-762 order et al. [35]. Bacterial cells were lysed with lysozyme and protease [36], embedded in plugs, digested with the restriction endonuclease SfiI (New England Biolabs, Ipswitch, MA, USA) and electrophoresed in a CHEF DRII apparatus (Bio-Rad,
Hercules, CA, USA) at 11°C with a pulse time of 5–20 s for the first 20 h and 1–5 s for the following 18 h. Annotation and pair-wise alignment analysis Gene prediction from the complete sequence was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP; http://www.ncbi.nlm.nih.gov/genomes/static/pipeline.html). Several of the suggested errors were revised manually. Pseudogenes that were identified by PGAAP were checked using the read-mapping correction described above. Genomic information, such as nucleic acid variations and circular representation, was analyzed using IMC-GE software (Insilicobiology, Yokohama, Japan). A BLASTN homology search [37] was performed for the whole chromosome sequences of C. pseudotuberculosis Niclosamide FRC41 (accession no. NC_014329), C. ulcerans 0102, and C. diphtheriae NCTC 13129 (accession no. NC_002935). Aligned images of the homologous regions were visualized with the ACT program [38]. Phylogenetic analysis Phylogenetic analyses of all nucleotide sequences were conducted using
the neighbor-joining method with 1,000-times bootstrapping in ClustalW2 [39]. FigTree ver. 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/) software was used to display the generated tree. Nucleotide sequence accession numbers The complete chromosome sequence for the C. ulcerans 0102 strain has been deposited in the DNA Data Bank of Japan (DDBJ; accession no. AP012284). Acknowledgments The authors are grateful to Akio Hatanaka, Atsuhiro Tsunoda and Kenji Ooe for the 0102 clinical isolate. This work was supported by grants for Research on Emerging and Re-emerging Infectious Diseases (H23 Shinko-Ippan-007 and H22-Shinko-Ippan-010), from the Ministry of Health, Labour and Welfare, Japan. Electronic supplementary material Additional file 1: Circular representation of the C. ulcerans 0102 genome.