DNA preparation, genome sequencing, and assembly
E. coli was inoculated into Luria Bertani broth (BD, China) and grown at 37°C with shaking for at least 12 h. Cells were collected by centrifugation, and genomic DNA (gDNA) was extracted using a Takara MiniBest Genomic DNA Extraction kit (Takara, China). DNA quality was measured by a NanoPhotometer (Implen, Germany) and a Qubit fluorometer (dsDNA HS) kit (Life Technologies). Indexed genomic libraries were prepared with the Nextera XT kit (Illumina, CA), and sequenced on Illumina MiSeq using 2×300 bp chemistry. Post-processed reads were assembled using SPAdes Genome Assembler version 3.8.1-Linux (Bankevich et al., 2012; Bolger, Lohse, & Usadel, 2014). Assembly quality was assessed by both custom scripts and abyss-fac command in ABySS (www.bcgsc.ca/platform/bioinfo/software/abyss) to determine N50, total length of contigs, and other parameters. Next-generation sequencing (NGS) data were deposited in the National Center for Biotechnology Information (NCBI) database under the Sequence Read Archive (SRP256501) accession (BioProject: PRJNA625565).