gDNA-seq of Escherichia coli: engineered fermenting strain
Strains were grown overnight in LB medium supplemented with 20 mM glucose and 10 mM acetate. The Macherey-Nagel NucleoSpin Microbial DNA purification Kit (Macherey-Nagel, Dren, Germany) was used to extract the genomic DNA. Microbial short insert PCR-free library construction for single-nucleotide variant detection and generation of 150 bp paired-end reads on an Illumina HiSeq 3000 platform were performed by Novogene (Cambridge, UK). Breseq (Barrick Lab, Texas)59 was used to map the obtained reads to the reference genome of E.coli MG1655 (GenBank accession no. U00096.3). With the algorithms supplied by the software package, we identified single-nucleotide variants (with >50% prevalence in all mapped reads) and regions more than 2 standard coverage deviations from the global median coverage.