Alignment of multiple complete genomes suggests that gene rearrangements may contribute towards the speciation of Mycobacteria.

To more accurately define the taxonomic relationships among species belonging to the genus Mycobacterium we have applied and compared three complete genome sequence comparison procedures to existing systems. These included a nucleotide sequence comparison including both coding and no-coding regions of the genome and two genomic-order comparisons using MAUVE and M-GCAT software to provide comparative gene synteny. These methods clearly differentiated a panel of genomes from reference mycobacterial species. Overall, the speciation of bacteria through determination of gene rearrangements were consistent with the gold standard method for species definition in bacteria, DNA-DNA hybridization however within the context of this system, individual components of the Mycobacterium tuberculosis complex (MTBC) did not show sufficient diversity to classify them as a separate species. The high number of gene rearrangements observed between the species tested suggests that gene reorganization of the genome represents an important contributor to speciation within the genus Mycobacterium and other related genera. The absence of rearrangements amongst MTBC supports their consideration as a single genospecies. Some gene rearrangements provided clear internal synteny between genomes of mycobacterial strains belonging to a same species and we suggest these could be used to classify subspecies.