Synteny plots using the BLAST Score Ratio method (Rasko et al. 2005). (A) ATCC 13124 vs. SM101. (B) ATCC 13124 vs. Strain 13. (C) SM101 vs. Strain 13. Each plot point represents a single peptide in the indicated C. perfringens genome pair. The color of each point indicates the level of similarity of that peptide in each genome pair, according to Rasko et al. (2005). Arrows indicate the 242,969-bp island.

Comparative analysis of each C. perfringens genome. (A) ATCC 13124; (B) SM101; (C) Strain 13. For each genome, data are from outermost circle to innermost. (Circles 1 and 2) Tick marks represent predicted coding sequences on the plus strand (circle 1) and minus strand (circle 2) colored by cellular role. Role categories and colors are as follows: amino acid biosynthesis, violet; biosynthesis of cofactors, prosthetic groups and carriers, light blue; cell envelope, light green; cellular processes, red; central intermediary metabolism, brown; DNA metabolism, gold; energy metabolism, light gray; fatty acid and phospholipid metabolism, magenta; protein synthesis and fate, pink; biosynthesis of purines, pyrimidines, nucleosides, and nucleotides, orange; regulatory functions and signal transduction, olive; transcription, dark green; transport and binding proteins, blue–green; other categories, salmon; unknown function, gray; conserved hypothetical proteins, blue; hypothetical proteins, black. (Circles 3 [blue] and 4 [red]) Genes identified by MUMmer analysis to be present in one genome but absent at that position in one other genome: (A) Circle 3: present in ATCC 13124 and absent in Strain 13; Circle 4: present in ATCC 13124 and absent in SM101. (B) Circle 3: present in SM101 but absent in Strain 13; Circle 4: present in SM101 but absent in ATCC 13124. (C) Circle 3: present in Strain 13 but absent in ATCC 13124; Circle 4: present in Strain 13 but absent in SM101. Circle 5: Phage genes (green), capsule-associated genes (purple) and IS elements (black). Circle 6: %G+C. Circle 7: χ²of trinucleotide composition.

Gel mobility shift assay of VirR binding to novel putative VirR boxes from C. perfringens ATCC 13124 and SM101. Varying amounts of VirR protein from strain 13 (VirR₁₃) was used in A, whereas either no protein (NP) or 1.0 μg of either VirR₁₃ or the VirR protein from SM101 (VirR₁₀₁) was added in B. The genes downstream of the putative VirR boxes are shown above each gel section. The pfoA gene from strain 13 was used as the positive control. The respective perfringolysin O (PFO) titers obtained when the various VirR box regions fused to a pfoA gene were introduced into a pfoA mutant (Cheung and Rood 2000) are indicated below the gel.