The rate, spectrum and effects of spontaneous mutation in bacteria with multiple chromosomes

Despite their essentiality for evolutionary change and role in many diseases, spontaneous mutations remain understudied because of both biological and technical barriers. Prokaryotic mutation biases are especially understudied and no studies have been conducted on bacteria with multiple chromosomes, leaving major gaps in our understanding of the role of genome content and structure on mutation. The application of mutation accumulation lines to whole-genome sequencing offers the opportunity to study spontaneous mutations in a wide range of prokaryotic organisms. Here, we present a genome-wide view of molecular mutation rates and spectra in Burkholderia cenocepacia, Vibrio fischeri, and Vibrio cholerae, three bacterial species that harbor multiple chromosomes but differ dramatically in %GC-content. We demonstrate both general and species specific biases in spontaneous mutation rates and spectra, while also highlighting how some mutational biases vary within within genomes. We then study the distribution of effects of spontaneous mutations in B. cenocepacia, illustrating that most mutations have little or no effect on fitness and those that do are mostly deleterious across multiple environments. Overall, this body of work offers unprecedented insight into the rate, spectrum, and fitness effects of spontaneous mutations in three prokaryotic organisms whose genomes harbor multiple circular chromosomes, a common but underappreciated bacterial genome architecture.