Fig. 1

Maximum likelihood phylogeny of MTB genomes. Phylogenomic tree based on concatenated alignment (3973 amino-acid positions) of up to 400 ubiquitous conserved proteins identified with PhyloPhlAn [34]. Archaeal genomes (accession numbers CP001719 and CP000678) were used as the outgroup. Red and purple denote MTB genomes from this study and from published MTB genome sequences, respectively. Bootstrap values are indicated with black circles (>75% support from 100 resamples). Detailed characteristics of genome sequences recovered in this study are summarized in Supplementary Table 2 (color figure online)