The genus Mycobacterium comprises more than 120 species; among them the saprophytes that adopted for free living lifestyle. Others are contagious, infectious and cause dangerous diseases for human and animals . Moreover, the availability of complete genome sequences of these important pathogens provided a wealth of information that could enable understanding the mechanisms of evolution, pathogenesis and systematically potential targets of drug discovery . In general, the mycobacteria belong to the phylum of Actinobacteria that are characterized by their large genome size and high GC content  and owing to their different lifestyles and environmental niches, the sizes of their genomes are varied .
Remarkably, the pathogenic slow growing mycobacteria had undergone to genome reduction  and consequently, they have a single rRNA operon and a low number of tRNA, comparing with the RGM . In this context, the loss of genes played an important role in the evolution of slow growing mycobacterial pathogens  and some of those genomes were suffered of an extensive genome downsizing like the MLP complex . On otherwise the members of MTBC were subjected to moderate genome reduction and concomitantly, acquired new genes towards the speciation to the parasitic life style in mammalian macrophages.
With the considerable genome size differences among the species included in this study, the number of added new genes per genome has increased the pan genome and the discovery of new genome sequences could add new genes to the current pan genome.
Unsurprisingly, the results of the core genome are in correlation with a previous experimental study realized by Marmiesse et al., in which they have estimated about 1439 genes as minimal set of conserved genes in the core genome of MTB and MLP, among them 219 genes that code for proteins show no similarity with proteins from other mycobacterial species . Consequently, this approach could help in the designation of new TB vaccines as reported by Jungblut et al..
In reality, one genome sequence is not enough for the development of a valuable vaccine and the definition of pan and core genome can provide a new insight for attaining this goal.
Even more, the comparative genomic analysis of predicted proteome by BLAST matrix showed a high similarity among MTB strains as already reported . The similarity values between MTB strains, M.bovis and attenuated M. bovis BCG vaccine strains were reasonable and the slight difference between the two vaccine strains (96.7%, 97.1%) could be attributed to the lack of RD 14 and the restricted duplication DU1 in the BCG Pasteur strain . Interestingly, the similarity between the MTBC and M.marinum was ranged between 47.0–47.7%. Regardless of the bigger genome size of M. Marinum, the close relatedness between those two species was documented and 3000 orthologs were shared between both genomes . This support the hypothesis of the decendy of MTB from an environmental Mycobacterium and due to the genome downsizing and the acquisition of new genes by HGT [14, 38], their capability of parasitism was evolved towards the mammalian macrophages [14, 37].
M ulcerans Agy99, which evolved from the same ancestor of M. marinum and has shown a less similarity with MTBC members (43%) and notably, this bacterium suffered of deletions, mainly, in the ESX1 locus , which is present in MTB and M marinum.
Significantly, M. aviums sp. Paratuberculosis strain K-10 with more than 3,000 homologous genes with MTB  showed a less similarity and the least similarity was found with the complex MLP and this could be attributed to the loss of PE_PGRS proteins in both of those species , Furthermore, the absence of many genes in MAV and the presence of pseudogenes in MLP elucidate the specificity of their virulence, tropism, the ability of cultivation and drug susceptibility pattern .
For better understanding the evolution of mycobacterial strains a phylogenetic tree was constructed based on 16 rRNA sequences, which allows the identification of most species within the genus Mycobacterium and can separate between the slow and RGM  and can be used for the systematic phylogeny analysis .
Unsurprisingly, the results of phylogeny analysis were in correlation with the previous results of genomic analysis of predicted proteome, which leads to an assertion that the ancestral MTBC and M. marinum genomes might be descended from the same ancestry owing to their close genetic relationship and phylogenetic relatedness.
Markedly, before the evolutionary bottleneck and clonal expansion of MTB members, the ancestral M. prototuberculosis species had acquired the particular Rv0986-8 virulence operon by HGT from an alpha proteobacterium  and evidently this operon still exists only in MTBC members.
Moreover, our study confirmed the high phylogenetical relationship among: MTBC, M.marinum- ulcerans, MAV and MLP complex, showing that the pathogenic slow growing mycobacteria define a distinct and common line of evolutionary descent from a free living bacterium.
Interestingly, the RGM have also acquired different genes toward the speciation to their environmental niches, like the acquisition of PAH Catabolism Genes in: M sp.MCS, M gilvum PYR-GCK, M sp. JLS, M sp KMS and M vanbaalenii PYR-1) , which enabled them to degrade polycyclic aromatic hydrocarbons. Significantly, many of RGM are ubiquitous in the environment and could become pathogenic for humans and induce opportunistic incurable infections like, M. abscessus and M. smegmatis due to their resistance against bactericidal agents.
Simultaneously, those RGM still share some conserved genes with the slow growing pathogenic mycobacteria, like the locus ESX3 which is highly conserved among all mycobacterial species  and as a result of comparative genomics this locus was exploited as a recombinant M. smegmatis vaccine against MTB .
Thus, the combination of different sets of computational genome, proteome and phylogeny analysis could easily visualize the evolutionary events and similarity relationships between mycobacterial species, which could help for better improving new diagnosis approaches and vaccines against TB and other mycobacterial diseases.