Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

PATANÉ JS; MARTINS J; BEATRIZ CASTELÃO A; NISHIBE C, ; MONTERA L, ; BIGI F.; ZUMÁRRAGA MJ; CATALDI AA, ; FONSECA JUNIOR A, ; ROXO E, ; LUIZA A,; OSÓRIO AR, ; JORGE UFMS KS, ; THACKER TC, ; ALMEIDA NF,; ARAÚJO FR, ; SETUBAL JC.

Genome biology and evolution

Oxford University Press

Lugar: Oxford; Año: 2017

Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild anddomesticated vertebrate livestock as well as humans. A comparison of the five M. bovis completegenomes from UK, South Korea, Brazil and USA revealed four novel large-scale structuralvariations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizingthis effect, we obtained a tree that better agrees with sampling locality. Results supported arelatively basal position of African strains (all isolated from Homo sapiens), confirming thatAfrica was an important region for early diversification and that humans were one of the earliesthosts. Selection analyses revealed that functional categories such as "Lipid transport andmetabolism", "Cell cycle control, cell division, chromosome partitioning" and "Cell motility"were significant for the evolution of the group, besides other categories previously described,showing importance of genes associated with virulence and cholesterol metabolism in theevolution of M. bovis. PE/PPE genes, many of which are known to be associated with virulence,were major targets for large-scale polymorphisms, homologous recombination, and positiveselection, evincing for the first time a plethora of evolutionary forces possibly contributing todifferential adaptability in M. bovis. By assuming different priors, USA strains originated andstarted to diversify around 150 - 5,210 ya. By further analyzing the largest set of USA genomesto date (76 in total), obtained from 14 host species, we detected that hosts were not clustered inclades (except for a few cases), with some faster-evolving strains being detected, suggesting fastand ongoing re-infections across host species and therefore the possibility of new bovinetuberculosis outbreaks.