Figure 3

Supermatrix phylogenomic trees (General Time Reversible model with Gamma substitution rate, include all codon positions, complete deletion option). (A) Fifty-gene tree. (B) Three-gene tree. Phylogenetic trees generated from the concatenation of the selected genes, constructed with the maximum likelihood method with boostrap values at important branches (1,000 bootstrap replicates). As shown in (B), the concatenation of three genes is sufficient to construct a phylogenetic tree showing subspecies classification similar to that in the supermatrix tree of fifty genes. As anticipated, of the 12 M. abscessus isolates analysed, only M24 is classified as M. bolletii, supported with 100% bootstrap support. M93, M94 and M152 are classified as M. abscessus sensu stricto and others as M. massiliense.