Complete Genome Sequencing of Mycobacterium bovis SP38 and Comparative Genomics of Mycobacterium bovis and M. tuberculosis Strains

Abstract

<i>Mycobacterium bovis</i> causes bovine tuberculosis and is the main organism responsible for zoonotic tuberculosis in humans. We performed the sequencing, assembly and annotation of a Brazilian strain of <i>M. bovis</i> named SP38, and performed comparative genomics of <i>M. bovis</i> genomes deposited in GenBank. <i>M. bovis</i> SP38 has a traditional tuberculous mycobacterium genome of 4,347,648 bp, with 65.5% GC, and 4,216 genes. The majority of CDSs (2,805, 69.3%) have predictive function, while 1,206 (30.07%) are hypothetical. For comparative analysis, 31 <i>M. bovis</i>, 32 <i>M. bovis</i> BCG, and 23 <i>Mycobacterium tuberculosis</i> genomes available in GenBank were selected. <i>M. bovis</i> RDs (regions of difference) and Clonal Complexes (CC) were identified <i>in silico</i>. Genome dynamics of bacterial groups were analyzed by gene orthology and polymorphic sites identification. <i>M. bovis</i> polymorphic sites were used to construct a phylogenetic tree. Our RD analyses resulted in the exclusion of three genomes, mistakenly annotated as virulent <i>M. bovis</i>. <i>M. bovis</i> SP38 along with strain 35 represent the first report of CC European 2 in Brazil, whereas two other <i>M. bovis</i> strains failed to be classified within current CC. Results of <i>M. bovis</i> orthologous genes analysis suggest a process of genome remodeling through genomic decay and gene duplication. Quantification, pairwise comparisons and distribution analyses of polymorphic sites demonstrate greater genetic variability of <i>M. tuberculosis</i> when compared to <i>M. bovis</i> and <i>M. bovis</i> BCG (<i>p</i> ≤ 0.05), indicating that currently defined <i>M. tuberculosis</i> lineages are more genetically diverse than <i>M. bovis</i> CC and animal-adapted MTC (<i>M. tuberculosis</i> Complex) species. As expected, polymorphic sites annotation shows that <i>M. bovis</i> BCG are subjected to different evolutionary pressures when compared to virulent mycobacteria. Lastly, <i>M. bovis</i> phylogeny indicates that polymorphic sites may be used as markers of <i>M. bovis</i> lineages in association with CC. Our findings highlight the need to better understand host-pathogen co-evolution in genetically homogeneous and/or diverse host populations, considering the fact that <i>M. bovis</i> has a broader host range when compared to <i>M. tuberculosis</i>. Also, the identification of <i>M. bovis</i> genomes not classified within CC indicates that the diversity of <i>M. bovis</i> lineages may be larger than previously thought or that current classification should be reviewed.