Mutation accumulation and whole-genome sequencing of laboratory strains of Escherichia coli

This study aimed to understand the mutation rates and mutation spectra of strains of Escherichia coli K-12 substrain MG1655 lacking components of the mismatch repair pathway. Three strains, each carrying a complete deletion of a single gene (mutH, mutL, or mutS) involved in mismatch repair, were evolved in the laboratory starting from a single ancestral clone each. Twenty replicate populations were founded for each strain, and evolved under a mutation accumulation (MA) regime for 50 days, with daily single-colony bottlenecks and tranfers onto fresh medium. At the end of the experiment, a single clone was chosen randomly from each replicate population, and cryopreserved (in 30% glycerol at -80C) for further analysis. To determine mutation rates and spectra, pooled whole-genome sequencing was performed for each strain. Genomic DNA from the final time-point clones was extracted and quantified. , Then, equal amounts of genomic DNA was pooled together for the 20 replicates corresponding to each strain. Thus, three pools were obtained, one each for mutH, mutL, and mutS. Paired-end libraries for whole genome sequencing were prepared from each pool, and also from the three ancestral clones. Libraries were sequenced on the Illumina MiSeq platform using the 2x250 paired-end V2 reaction chemistry. This SRA submission contains the .fastq files that emerged from this sequencing experiment.