Figure 2

Local collinear blocks (LCBs) between chromosomal sequences of the two strains of Streptococcus mutans. (a) Representation of the whole 32 local collinear blocks (LCBs) between chromosomal sequences of the two strains of Streptococcus mutans, UA159 and NN2025, was generated by MAUVE software at a minimum weight of 411. The S. mutans UA159 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. The 32 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 homologous backbone DNA sequence without rearrangements. Black horizontal bars indicate rearrangement regions and strain-specific regions analyzed in detail (see additional files 2 and 3). Blue region numbers and bars indicate NN2025-specific regions, pink region numbers and bars indicate UA159-specific regions, and black region numbers and bars indicate variable regions. Distributions of regions 1–25 are analyzed by long-PCR in 97 S. mutans strains including strains NN2025 and UA159 (see additional files 4 and 6). A dot plot to compare genome structure of these strains is also shown in Figure 6. (b) Alignment of the two genomes is generated by artificially correcting for the inversion of NN2025 at the rrn-comX region by the PROmer of MUMmer software and GenomeMatcher software (green bar). Similarity is shown by color code as represented in this figure. Blue region numbers and arrows indicate NN2025-specific regions, pink region numbers and arrows indicate UA159-specific regions, and black region numbers and arrows indicate variable regions.