Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in <i>Bordetella pertussis</i> and <i>Mycobacterium tuberculosis</i>.

ABSTRACT: Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We dem

SUBMITTER: Abrahams JS 

PROVIDER: S-EPMC8942028 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature