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).