Modeling Bacterial Evolution with Comparative-Genome-Based Marker Systems: Application to Mycobacterium tuberculosis Evolution and Pathogenesis
| العنوان: | Modeling Bacterial Evolution with Comparative-Genome-Based Marker Systems: Application to Mycobacterium tuberculosis Evolution and Pathogenesis |
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| المؤلفون: | Mark Kokoris, Megan Murray, David Alland, Kim Dix, Jonathan A. Eisen, Manzour Hernando Hazbón, M. Donald Cave, Robert D. Fleischmann, Andreas Duesterhoeft, Claire M. Fraser, Thomas S. Whittam |
| المصدر: | Journal of Bacteriology. 185:3392-3399 |
| بيانات النشر: | American Society for Microbiology, 2003. |
| سنة النشر: | 2003 |
| مصطلحات موضوعية: | Population, Single-nucleotide polymorphism, Computational biology, Polymorphism, Single Nucleotide, Microbiology, Genome, Evolution, Molecular, Mycobacterium tuberculosis, Bacterial Proteins, Phylogenetics, Humans, SNP, Computer Simulation, education, Molecular Biology, Phylogeny, Molecular Biology of Pathogens, Genetics, education.field_of_study, Polymorphism, Genetic, biology, Phylogenetic tree, Strain (biology), Computational Biology, biology.organism_classification, DNA Transposable Elements, Genome, Bacterial |
| الوصف: | The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M . tuberculosis . Phylogenetic analysis using these “comparative-genome markers” (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared “reference strains.” Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M . tuberculosis , we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI “C” strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS 6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure. |
| تدمد: | 1098-5530 0021-9193 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c5742bfcddf45031787fa57583a0e41a https://doi.org/10.1128/jb.185.11.3392-3399.2003 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....c5742bfcddf45031787fa57583a0e41a |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 10985530 00219193 |
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