Genome sequencing has reinvigorated the infectious disease research feld, shedding light on disease
epidemiology, pathogenesis, host–pathogen interactions and also evolutionary processes exerted
upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its
animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model
of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly
evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this
work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by
70 M. bovis from diferent lineages (European and African) to gain insights into the evolutionary forces
that shape genetic diversifcation in M. bovis. Three distinct approaches were used to estimate signs
of recombination. Globally, a small number of recombinant events was identifed and confrmed by
two independent methods with solid support. Still, recombination reveals a weaker efect on M. bovis
diversity compared with mutation (overall r/m= 0.037). The diferential r/m average values obtained
across the clonal complexes of M. bovis in our dataset are consistent with the general notion that
the extent of recombination may vary widely among lineages assigned to the same taxonomical
species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a
topic of further efort in future comparative genomics studies for which WGS of large datasets from
diferent epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n= 42) from
a multi-host TB endemic scenario was then subjected to additional analyses, with the identifcation
of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP).
The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon
synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important
evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched
into “lipid metabolism”, “cell wall and cell processes” and “intermediary metabolism and respiration”
functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer
look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA
repair, replication and recombination) system revealed a global average negative value for Taijima’s
D neutrality test, suggesting that past selective sweeps and population expansion after a recent
bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle
with the host.info:eu-repo/semantics/publishedVersio
