Systematic comparative functional pan-genome analysis reveals epistasis- and pleiotropy-dependent evolutionary behaviors for polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium

The genus Mycobacterium is of great interest for medical and biotechnological issues. In this study, we conducted a systematic comparative functional pan-genomic analysis to generate a useful mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype with pan-genomic perspective of the evolutionary events, standing with the environmental challenges. Phylogenic, phenotypic, and genomic information of 27 complete genome-sequenced mycobacteria were systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with pan genomic concept at network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. The PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH-degraders. A series of functional pan-genomic analyses provided conserved/unique genomic evidences for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns by HGT/deletion events hypothesize a plausible evolutionary path, an epistatic-based birth and pleiotropic-dependent death, for bacterial PAH metabolism in the genus Mycobacterium. Our findings suggest that when selection acts on evolution of PAH metabolism, only a very small fraction of trajectories is likely to be observed, owing mainly to combination of the double-faced phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary behaviors. Evolutionary constraints on the selective choice of trajectories like those seen in PAH-degrading phenotype are likely to apply to the evolution of other phenotypes in the genus Mycobacterium, which is essential to better characterizing mycobacterial communities associated with medical or bioengineering applications.