Time-series Genomic Analysis of Evolving E. coli

Genomic DNA from the starting culture and 24 samples of evolving bacterial populations in time series (6 reactors ×4 days) was extracted from cell pellets with the Sigma Aldrich GenElute Bacterial Genomic DNA kit (NA2110). Sequencing libraries were prepared with the Illumina TruSeq DNA PCR-Free High Throughput Library Prep kit (#20015963) according to the manufacturer’s instructions. DNA was sequenced with the Illumina NextSeq 500 using 2×150 reads to reach up to 500–1000-fold genomic coverage in each sample (see Table S1, available in the online version of this article, for data quality and statistics). Reads were cleaned from adapter sequences, poly-G sequences and were trimmed by Phred base quality score with the Trimmomatic [30 (link)] (with ‘SLIDINGWINDOW : 4 : 15 HEADCROP : 10 CROP : 145 MINLEN : 65′ parameters). Cleaned reads were mapped onto an E. coli BW25113 genome downloaded from the PATRIC database (genome ID 679895.18) [31 (link)] with the BWA aligner [32 (link)] (using the ‘-M’ parameter). Alignments were corrected with lofreq viterbi [33 (link)] (using ‘--keepflags’ parameter). Quality scores were recalibrated with GATK BaseRecalibrator [34 (link)]. Sequencing data in fastq format have been deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), BioProject PRJNA472810.