Research article
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content
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* Corresponding author: Ichiro Nakagawa ichiro-n.bac@tmd.ac.jp
1 Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
2 Department of Pediatric Dentistry, Osaka University Graduate School of Dentistry, 1-8 Yamada-oka, Suita, Osaka 565-0871, Japan
3 Divison of Information Biotechnology, Department of Bioinformation Engineering, Tokyo Institute of Technology School and Graduate School of Bioscience and Biotechnology, 4259 Nagatsuta-cho, Midori-ku, Yokohama Kanagawa 226-8501, Japan
4 Human genome Center, Institute of Medical Science, The University of Tokyo
5 Department of Oral and Molecular Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, 565-0871, Japan
6 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
7 Research Collaboration Center on Emerging and Reemerging Infections (RCC-ERI) 6F, Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Muang Nonthaburi, 11000, Thailand
8 Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
BMC Genomics 2009, 10:358 doi:10.1186/1471-2164-10-358
Published: 5 August 2009Additional files
Additional file 1:
General features of S. mutans strains NN2025 and UA159.
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Additional file 2:
S. mutans NN2025 specific ORFs. Different regions within the PCR region are shown in different colours and correspond to the regions shown in Figure 2. No coloring in the PCR region indicates the absence of the ORF in the regions in Figure 2.
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Additional file 3:
S. mutans UA159-specific ORFs. Different regions within PCR region are shown in different colors and correspond to the regions shown in Figure 2. No coloring in the PCR resion indicates the absence of the ORF in the regions in Figure 2.
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Additional file 4:
Long-PCR analyses of genomic rearrangement region and insertion/deletion regions of S. mutans strains.
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Additional file 5:
Primers used for detection of rearrangement and strain-specific regions in S. mutans strains. Each strain-specific region is visualized as a black bar in Figure 2.
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Additional file 6:
Characteristics of S. mutans reference strains and clinical isolates used in this study.
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Additional file 7:
Cluster analysis based on strain-specific regions showing the relationship between S. mutans strain NN2025, UA159 and 95 clinical isolates. Long-PCR results were converted to numerical values according to the length of the PCR products, then complete linkage clustering was performed on CLUSTER software and visualized with Java Tree view software (contrast value; 0 to 3.0).
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Additional file 8:
Characteristics of CRISPR loci found in S. mutans NN2025. The nomenclature, leader sequence, repeat sequence, number of repeats, and similarity were determined based on the method of Horvath et al. [64] with slight modifications (see Methods for details).
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Additional file 9:
Sequence similarities of the existing CRISPR spacers in S. mutans NN2025. The spacer similarities were determined by BLASTN against viruses including bacteriophage or bacteria databases (see Methods). No description in "origin" or "BLAST E-value" indicates that no similarity was found in the database.
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Additional file 10:
Distribution of CRISPR-2 (Smut2b; Sthe3 family)-associated repeat sequences in genus Streptococcus. Repeat sequences in the CRISPR-2 homologous region (Sthe3 family) were found in 19 of 32 streptococcal genomes (see Methods; for NN2025, see additional file 8). Similarities of the direct repeat sequence of the strain NN2025 (Sthe3 family) were examined by BLASTN against each genome as a target database. The number of repeats was determined based on Horvath et al. [64] (see Methods).
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Additional file 11:
Distribution of CRISPR-2 (Smut2b)-associated repeat sequences in genus Streptococcus. Repeat sequences in the CRISPR-2 homologous region (Smut2b; Sthe3 family) found in streptococcal genomes except S. mutans NN2025 (15/31 strains; see Methods). Similarities were examined by BLASTN against each genome as a target database. The number of repeats was determined as described by Horvath et al. [64] (see Methods).
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Additional file 12:
Venn diagrams for the clustered gene groups in S. mutans species and eight other streptococcal species. All the predicted ORFs from the 32 streptococcal strains were clustered into groups based on a threshold of maximum E-value = 10-5 in the reciprocal BLATP analysis to compare the numbers of species-specific and -shared gene groups and those shared with S. mutans species. The number in the figure was the number of the gene groups, not of the ORFs (see Methods for details).
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Additional file 13:
Specific gene groups shared in oral streptococci. All the predicted ORFs from the 32 streptococcal strains were clustered into groups based on a threshold of maximum E-value = 10-5 in the reciprocal BLATP analysis to extract the ORF(s) of gene groups specific for oral streptococci (S. mutans, S. sanguinis, and S. gordonii). The predicted function is assigned based on the COG classification (see Methods for details).
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Additional file 14:
Comparison of genomic shuffling between two strains of S. mutans (N2025 and UA159) and three strains of S. pyogenes (SSI-1, SF370 and Manfredo). A MAUVE representation of the total 64 local collinear blocks (LCBs) between chromosomal sequences of the S. mutans strains and S. pyogenes strains, at a minimum weight of 144. The S. mutans NN2025 DNA sequence given on the forward strand is the reference against which the sequence of the NN2205 was aligned and compared. LCBs placed under the vertical bars represent the reverse complement of the reference DNA sequence. LCBs placed under the vertical bars represent the reverse complement of the reference DNA sequence. The 64 connecting lines between genomes identify the locations of each orthologous LCB in the two genomes. Unmatched regions within an LCB indicate the presence of strain-specific sequence. Each sequential block represents a homologous backbone DNA sequence without rearrangements.
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Additional file 15:
Genome comparison of each S. mutans with six S. pneumoniae strains based on the chromosomal organization of the strain NN2025 or UA159. Dot plots of S. mutans NN2025 vs. six S. pneumoniae strains and of S. mutans UA159 vs the same set of S. pneumoniae strains are presented, as generated by PROmer of MUMmer software and visualized with GenomeMatcher software [116](see Methods).
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Additional file 16:
Genome comparison of each S. mutans with three S. agalactiae strains based on the chromosomal organization of the strain NN2025 or UA159. Dot plots of S. mutans NN2025 vs. three S. agalactiae strains and of S. mutans UA159 vs. the same set of S. agalactiae strains are presented, as generated by PROmer of MUMmer software and were visualized with the GenomeMatcher software [116] (see Methods).
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Additional file 17:
Genome comparison of each S. mutans with three S. thermophilus strains based on the chromosomal organization of the strain NN2025 or UA159. Dot plots of S. mutans NN2025 vs three S. thermophilus strains and of S. mutans UA159 vs. the same set of S. thermophilus strains are presented, as generated by PROmer of MUMmer software and visualized with the GenomeMatcher software (see Methods).
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Additional file 18:
Genome comparison of each S. mutans with two S. agalactiae strains, S. sanguinis SK36, S. gordonii Challis CH11, S. equi zooepidemicus MGCS10565 based on the chromosomal organization of the strain NN2025 or UA159. Dot plots of S. mutans NN2025 vs. two S. agalactiae strains, S. sanguinis SK36, S. gordonii Challis CH11, and S. equi zooepidemicus MGCS10565 and of S. mutans UA159 vs. the same set of streptococcal strains are presented, as generated by PROmer of MUMmer software and were visualized with the GenomeMatcher software (see Methods).
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Additional file 19:
Lengths of locally collinear blocks (LCBs) shared by the nine Streptococcal species. Block lengths are taken from the S. mutans NN2025 genome. Lengths of LCBs were determined using SPRING software.
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