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. 2015 Feb 14;15:21. doi: 10.1186/s12862-015-0302-8

Figure 11.

Figure 11

Gain and loss of PAH-degrading genes in the genus Mycobacterium . Boxes on nodes and tips for the phylogeny show numbers of the PAH-degrading gene groups and numbers of the groups with more than one member at least, respectively. Numbers and dots on branches indicate the gains and losses of twenty three PAH-degrading gene groups and four types of RHO groups, respectively, with blue indicating an overall gain and red an overall loss. Roman numerals in the dots indicate type (types II, IV, V and X) of the RHO systems based on Kweon’s classification [67,69]. The 27 mycobacteria are color shaded according to their lifestyle: green, free-living; blue, facultatively-host-associated; red, obligately intracellular. OH-DH4, alcohol dehydrogenase 4; RCD, ring-cleavage dioxygenase; PcaG, the alpha subunit of protocatechuate 3,4-dioxygenase; RHO, ring-hydroxylating oxygenase; OH-DH2, alcohol dehydrogenase 2; PcaI, 3-oxoadipate CoA-transferase subunit A; PcaJ, 3-oxoadipate CoA-transferase subunit B; PcaL, 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylase.