The role of IS6110 in micro- and macroevolution of Mycobacterium tuberculosis lineage 2

Publication date: Available online 11 July 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Egor Shitikov, Andrei Guliaev, Julia Bespyatykh, Maja Malakhova, Sergey Kolchenko, Georgy Smirnov, Mathias Merker, Stefan Niemann, Igor Mokrousov, Elena Ilina, Vadim GovorunAbstractThe insertion sequence 6110 (IS6110) is the most studied transposable element in the Mycobacterium tuberculosis complex species. The element plays a significant role in genome plasticity of this important human pathogen, but still many causes and consequences of its transposition have not been fully studied. Here, we analyzed insertion sites for 902 Mycobacterium tuberculosis lineage 2 strains using whole-genome sequencing data. In total, 17,972 insertions were found, corresponding to 827 independent positions in the genome of the reference strain H37Rv. To trace the history of IS6110 expansion since proto-Beijing strains up to modern sublineages, we looked at the distribution of IS6110 across the genome-wide SNP-based phylogenetic tree. This analysis demonstrated a stepwise transposition of IS6110 that occurs by «copy-and-paste» mechanism. Additionally, we detected evolutionary-scale and sublineage-specific integration sites, which can be used for typing and for understanding the reasons for the success of the lineage. A significant part of such insertions affected the genes that are essential for the pathogen. Finally, we identified and confirmed deletions that occurred between differently ori...
Source: Molecular Phylogenetics and Evolution - Category: Molecular Biology Source Type: research