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dc.contributor.authorLibrado, Pablo
dc.contributor.authorVieira, Filipe G.
dc.contributor.authorSánchez-Gracia, Alejandro
dc.contributor.authorKolokotronis, Sergios-Orestis
dc.contributor.authorRozas, Julio
dc.date.accessioned2022-08-25T19:22:56Z
dc.date.available2022-08-25T19:22:56Z
dc.date.issued2014-06-05
dc.identifier.citationLibrado P, Vieira FG, Sánchez-Gracia A, Kolokotronis SO, Rozas J. Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families. Genome Biol Evol. 2014 Jun 5;6(6):1454-65. doi: 10.1093/gbe/evu117. PMID: 24904011; PMCID: PMC4079203.en_US
dc.identifier.eissn1759-6653
dc.identifier.doi10.1093/gbe/evu117
dc.identifier.pmid24904011
dc.identifier.urihttp://hdl.handle.net/20.500.12648/7514
dc.description.abstractSpecies of the genus Mycobacterium differ in several features, from geographic ranges, and degree of pathogenicity, to ecological and host preferences. The recent availability of several fully sequenced genomes for a number of these species enabled the comparative study of the genetic determinants of this wide lifestyle diversity. Here, we applied two complementary phylogenetic-based approaches using information from 19 Mycobacterium genomes to obtain a more comprehensive view of the evolution of this genus. First, we inferred the phylogenetic relationships using two new approaches, one based on a Mycobacterium-specific amino acid substitution matrix and the other on a gene content dissimilarity matrix. Then, we utilized our recently developed gain-and-death stochastic models to study gene turnover dynamics in this genus in a maximum-likelihood framework. We uncovered a scenario that differs markedly from traditional 16S rRNA data and improves upon recent phylogenomic approaches. We also found that the rates of gene gain and death are high and unevenly distributed both across species and across gene families, further supporting the utility of the new models of rate heterogeneity applied in a phylogenetic context. Finally, the functional annotation of the most expanded or contracted gene families revealed that the transposable elements and the fatty acid metabolism-related gene families are the most important drivers of gene content evolution in Mycobacterium.en_US
dc.language.isoenen_US
dc.publisherOxford University Press (OUP)en_US
dc.relation.urlhttps://academic.oup.com/gbe/article/6/6/1454/583471en_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectGeneticsen_US
dc.subjectEcology, Evolution, Behavior and Systematicsen_US
dc.subjectM. tuberculosisen_US
dc.subjectgene familiesen_US
dc.subjectgene gain and lossen_US
dc.subjectgene turnover ratesen_US
dc.subjectmaximum likelihooden_US
dc.subjectrate heterogeneityen_US
dc.titleMycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Familiesen_US
dc.typeArticle/Reviewen_US
dc.source.journaltitleGenome Biology and Evolutionen_US
dc.source.volume6
dc.source.issue6
dc.source.beginpage1454
dc.source.endpage1465
dc.description.versionVoRen_US
refterms.dateFOA2022-08-25T19:22:57Z
dc.description.institutionSUNY Downstateen_US
dc.description.departmentEpidemiology and Biostatisticsen_US
dc.description.degreelevelN/Aen_US


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Attribution 4.0 International
Except where otherwise noted, this item's license is described as Attribution 4.0 International