Bacterial genome structural variation: prevalence, mechanisms, and consequences

A vast number of bacterial genome sequences are publicly available. However, the majority were generated using short-read sequencing, producing fragmented assemblies. Long-read sequencing can generate closed assemblies, and they reveal that bacterial genome structure, the order and orientation of genes on the chromosome, is highly variable for many species. Growing evidence suggests that genome structure is a determinant of genome-wide gene expression levels and thus phenotype. We review this developing picture of genome structure variation among bacteria, the challenges for the study of this phenomenon, and its impact on adaptation and evolution, including virulence and infection.