Escherichia coli REL606 Raw sequence reads

In this study, we first sought to characterise the mutational changes that accompany a loss in fitness due to genetic bottlenecking in Escherichia coli. Using fitness measurements and whole-genome sequencing, we examined the evolutionary dynamics of ten independent mutation accumulation lines of a hypermutator E. coli population growing on nutrient rich, solid media. After 100 single-colony bottlenecks over approximately 4,000 generations, we found that severely bottlenecked lineages showed lower fitness than their ancestor and weakly bottlenecked controls, and had accumulated deleterious mutations in proteins spanning a wider range of cellular functions.Of the ten bottlenecked lines, one developed a higher mutation rate and succumbed to mutational meltdown during the course of the experiment. In order to characterise the molecular changes that accompany recovery from genetic bottlenecking, we cultured ten parallel lines of the mutational meltdown strain, taken from the last time point at which it was viable, and allowed it to grow competitively in broth culture. We observed a rapid, partial return to fitness followed by a levelling off of fitness improvements. We found parallelism in mutational patterns indicative of both repair of damaged protein coding genes and compensatory inactivation of other genes.