Fig. 2

Organization of the BCG Danish 1331 (07/270) genome, focusing on the DU1 and DU2. a Circular representation of the BCG Danish chromosome. The scale is shown in megabases on the outer black circle. Moving inward, the next two circles show forward (dark blue) and reverse (yellow) strand CDS (coding sequence). The next circle shows 3 rRNAs (5S, 16S and 23S; orange), 45 tRNAs (black), 1 tmRNA (ssrA; green) and 1 ncRNA (rnpB; dark green3), followed by 42 SNPs (red) detected between BCG Danish and Pasteur. The subsequent circle shows DU2-III (dark blue), DU1-Danish (purple) and RD (light blue, names of RD in black) that are typical for BCG Danish. The two inner circles represent G + C content and GC skew. b Organization of the two tandem duplications in BCG Danish and confirmation by PCR. The DU2 is made up by two repeats (R1 and R2), as well as the DU1-Danish (R3 and R4). Used primer pairs (1–8) to validate their organization are indicated. c Visual representation of the oriC with position and size of DU1-China, −Danish, −Pasteur and -Birkhaug. The table indicates which substrains have the DU1. d Copy-number analysis of genes (indicated in grey in subfigure c) in and surrounding the DU1 region for Pasteur 1173 ATCC 35734, Pasteur 1721 and Danish 1331 NIBSC 07/270. The represented data are averages (± SD) of four technical replicates