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Patterns and Processes of Mycobacterium bovis Evolution Revealed by Phylogenomic Analyses

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dc.contributor.authorPatane, Jose S. L.en
dc.contributor.authorMartins, Joaquim, Jr.en
dc.contributor.authorCastelao, Ana Beatrizen
dc.contributor.authorNishibe, Christianeen
dc.contributor.authorMontera, Lucianaen
dc.contributor.authorBigi, Fabianaen
dc.contributor.authorZumarraga, Martin J.en
dc.contributor.authorCataldi, Angel A.en
dc.contributor.authorFonseca Junior, Antonioen
dc.contributor.authorRoxo, Elianaen
dc.contributor.authorOsorio, Ana Luiza A. R.en
dc.contributor.authorJorge, Klaudia S.en
dc.contributor.authorThacker, Tyler C.en
dc.contributor.authorAlmeida, Nalvo F.en
dc.contributor.authorAraujo, Flabio R.en
dc.contributor.authorSetubal, Joao C.en
dc.date.accessioned2020-03-26T13:00:32Zen
dc.date.available2020-03-26T13:00:32Zen
dc.date.issued2017-03en
dc.description.abstractMycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as "Lipid transport and metabolism," "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 the evolution 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 positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis. By assuming different priors, US strains originated and started to diversify around 150-5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks.en
dc.description.adminPublic domain – authored by a U.S. government employeeen
dc.description.notesThis work was partially supported by the Brazilian Agency CAPES (grant number 3385/2013). J.S.L.P. and J.M. were supported by CAPES fellowships. J.C.S. was supported in part by a grant from CNPq (grant number 304881/2015-5). N.F.A. was supported by grants Fundect TO141/2016, TO007/2015, CNPq 305857/2013-4, 473221/2013-6, and CAPES 3377/2013.en
dc.description.sponsorshipBrazilian Agency CAPESCAPES [3385/2013]; CAPESCAPES [3377/2013]; CNPqNational Council for Scientific and Technological Development (CNPq) [304881/2015-5, 305857/2013-4, 473221/2013-6]; FundectFundect [TO141/2016, TO007/2015]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/gbe/evx022en
dc.identifier.issn1759-6653en
dc.identifier.issue3en
dc.identifier.pmid28201585en
dc.identifier.urihttp://hdl.handle.net/10919/97486en
dc.identifier.volume9en
dc.language.isoenen
dc.rightsCreative Commons CC0 1.0 Universal Public Domain Dedicationen
dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/en
dc.subjectMycobacterium bovisen
dc.subjectbovine tuberculosisen
dc.subjectphylogenomicsen
dc.subjectPE/PPE familyen
dc.subjectepidemiologyen
dc.titlePatterns and Processes of Mycobacterium bovis Evolution Revealed by Phylogenomic Analysesen
dc.title.serialGenome Biology and Evolutionen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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