title: Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region.
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 further identify a smaller segmental duplication of a different genomic region of a lab strain of H37Rv. The presence of multiple independent duplications of the same genomic region suggests either instability in this region, a selective advantage conferred by the duplication, or both. The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considered.
authors.affiliation: The Broad Institute, Cambridge, Massachusetts, United States of America.
authors.forename: Brian
authors.initials: B
authors.lastname: Weiner
authors.forename: James
authors.initials: J
authors.lastname: Gomez
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Victor
authors.forename: Robert M
authors.initials: RM
authors.lastname: Warren
authors.forename: Alexander
authors.initials: A
authors.lastname: Sloutsky
authors.forename: Bonnie B
authors.initials: BB
authors.lastname: Plikaytis
authors.forename: James E
authors.initials: JE
authors.lastname: Posey
authors.forename: Paul D
authors.initials: PD
authors.lastname: van Helden
authors.forename: Nicolass C
authors.initials: NC
authors.lastname: Gey van Pittius
authors.forename: Michael
authors.initials: M
authors.lastname: Koehrsen
authors.forename: Peter
authors.initials: P
authors.lastname: Sisk
authors.forename: Christian
authors.initials: C
authors.lastname: Stolte
authors.forename: Jared
authors.initials: J
authors.lastname: White
authors.forename: Sebastien
authors.initials: S
authors.lastname: Gagneux
authors.forename: Bruce
authors.initials: B
authors.lastname: Birren
authors.forename: Deborah
authors.initials: D
authors.lastname: Hung
authors.forename: Megan
authors.initials: M
authors.lastname: Murray
authors.forename: James
authors.initials: J
authors.lastname: Galagan
mesh_terms: D024881:Drug Resistance, Bacterial; D020440:Gene Duplication; D014644:Genetic Variation; D016680:Genome, Bacterial; D009169:Mycobacterium tuberculosis / Q000235:genetics*