Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region.

PloS One
Brian WeinerJames Galagan

Abstract

Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, and the finding of more functional genetic diversity than previously expected, there is a renewed interest in understanding the forces driving genome evolution of this important pathogen. Genetic diversity in M. tuberculosis is dominated by single nucleotide polymorphisms and small scale gene deletion, with little or no evidence for large scale genome rearrangements seen in other bacteria. Recently, a single report described a large scale genome duplication that was suggested to be specific to the Beijing lineage. We report here multiple independent large-scale duplications of the same genomic region of M. tuberculosis detected through whole-genome sequencing. The duplications occur in strains belonging to both M. tuberculosis lineage 2 and 4, and are thus not limited to Beijing strains. The duplications occur in both drug-resistant and drug susceptible strains. The duplicated regions also have substantially different boundaries in different strains, indicating different originating duplication events. We furthe...Continue Reading

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Citations

Jul 12, 2013·Future Microbiology·Kathryn T ElliottEllen L Neidle
Mar 26, 2014·Nature Reviews. Genetics·James E Galagan
Nov 2, 2016·Journal of Bacteriology·Pilar DomenechMichael B Reed
Aug 8, 2018·Antimicrobial Agents and Chemotherapy·Justin L KandlerJames E Posey
Nov 14, 2016·Microbiology Spectrum·Stefan NiemannPhilip Supply
Dec 3, 2014·Seminars in Immunology·Mireia Coscolla, Sebastien Gagneux

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Methods Mentioned

BETA
PCR
Illumina sequencing

Software Mentioned

Matlab scripts
custom
PhyML
BIONJ
Maq

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