Reconstruction of the evolutionary history of the PE and PPE gene families of the genus Mycobacterium. Schematic representation of the suggested evolutionary history of the PE and PPE gene families. The results of this study indicated that these genes were initially inserted into the ESAT-6 (esx) gene cluster region 1 after the duplication of the cluster, and have subsequently been duplicated along with the ESAT-6 regions. The expansion of the PE and PPE gene families have occurred in unison with the expansion of the ESAT-6 (esx) gene family, throughout the evolution of the genus. Members of the genus Mycobacterium investigated in this study, have diverged at the positions indicated. After each main duplication event involving a complete ESAT-6 (esx) gene cluster region, a number of secondary subduplications of the PE and PPE genes (in some cases associated with a copy of the ESAT-6 and CFP-10 genes, occurred from the newly duplicated ESAT-6 (esx) gene cluster region. The highly duplicated PE_PGRS and PPE-MPTR subfamilies originated after the divergence of the M. avium complex and M. leprae, respectively. Both families were present before the divergence of M. marinum/M. ulcerans and the M. tuberculosis complex.