2016 Volume 32 Issue 1 Pages 25-37
We generated and analyzed draft genomes for 42 Mycobacterium strains representing 30 different species to select core housekeeping proteins (HKPs) that would be useful for differentiating among closely related Mycobacterium species.
HKPs of Mycobacterium tuberculosis H37Rv were selected as reference proteins, and values (designated diversity values) representing the amino acid differences between these H37Rv HKPs and those of other individual Mycobacterium species were calculated for each HKP. From seven NCBI protein categories, we analyzed the 107 proteins commonly found in all 30 Mycobacterium species. We then selected the 12 most variable HKPs to construct a concatenated protein sequence (designated C12HKP). The average C12HKP diversity value for these 30 Mycobacterium species was 22.50%. Phylogenetic trees constructed with either C12HKP or C50RP (50 concatenated sequences from 50S and 30S ribosomal proteins) had reliable bootstrap values that were higher than those of a 16S rRNA gene tree. Of the three entities (C12HKP, 16S rRNA gene, and C50RP), C12HKP exhibited the greatest diversity. To differentiate among closely related species within the genus Mycobacterium, the C12HKP entity provided the most powerful and discriminating dataset.
