Abstract: Most studies of bacterial genetic diversity have focused on the metrics of SNPs and gene content. However, other types of genetic diversity exist, but are poorly studied, including genome arrangement and copy number variations. The application of long-read sequencing to the study of B. pertussis reveals that variation in genome structure dominates the genetic diversity of this species, providing a unique opportunity to understand its role in generating phenotypic diversity, and thus in driving evolution and adaptation of this re-emerging pathogen.
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