Figure 1.
Comparative phylogenetic analysis of strains under study and 12 whole genomes from the NCBI database.
Phylogenetic tree based on all SNPs of genomes was constructed using the Neighbor-Joining algorithm. Evolutionary distances were calculated using p-distance method.
Table 1.
Genotyping and drug resistance data of the B0/W148 strains sequenced in this study.
Figure 2.
Schematic representation of genome rearrangements' and primer design strategy.
Each local collinear block (LCB) corresponds to Table 2 and is represented by a different color.
Table 2.
Description of five local collinear blocks (LCBs) between H37Rv and W-148.
Figure 3.
Southern blot analysis of H37Rv and SP21 MTB strains.
Genomic DNA was digested with MluI and hybridized with the fluorescent labeled probes obtained by amplification. The probes are listed at the top of the lanes (from A to H). (A) Hybridization patterns of H37Rv strain. The order of probes corresponds to the order of complementary sequence sites in the genome of H37Rv. (B) Hybridization pattern of SP21 strains. The order of probes corresponds to the order of complementary sequence sites in the genome of H37Rv. (C) Hybridization patterns of SP21 strain. The order of probes is rearranged in accordance with the expected order of complementary sequence sites in the inverted genome (Supplementary Text S1). The merged bands from probes complementary to the boundaries of recombination junctions are boxed. M, marker strain Mt14323 (Mycobacterial Reference Laboratory, National Public Health Institute (Turku, Finland)).
Table 3.
Primers designed for analysis of genomic arrangement in studied MBT strains.
Figure 4.
Results of PCR verification of inversions.
Electrophoregram of PCR products obtained for MTB strains during the amplification with primer sets 1–8 (Table 3).(A) SP 21 B0/W148 Beijing strain and (B) SP 5 non-B0/W148 Beijing strain. Lanes 1–8 correspond to primer sets 1–8; M is a marker GeneRuler 100 bp Plus DNA Ladder (Fermentas, SM0324); K- is a negative control.
Figure 5.
Genome rearrangements' representation for W-148 Progenitor I like H37Rv, W-148 Progenitor II and W-148 genomes.
Each local collinear block (LCB) I–V is represented by a different color. Upside-down blocks (LCBs II and IV) represent the location of the reverse strand, which means an inversion has occurred. Asterisk indicates a terminus of a replication site. Terminus of a replication site was calculated based on GraphDNA (GC-skew mode) software [19].
Figure 6.
Schematic presentation of duplicated bases flanking the IS6110 insertion sites between LCBs II&III and III&IV.