Whole-Genome Sequencing and Annotation of E. coli

Whole-genome sequencing was performed on all strains. Briefly, single colonies were grown for 16 h in LB broth at 37 °C and bacterial DNA was extracted using a bacterial DNA extraction kit (Omega Bio-Tek, USA) according to the manufacturer’s instructions. Whole-genome sequencing was performed by Novegene (Novogene BioTech, Beijing, China) on an Illumina Novaseq platform. Genomes were assembled using Shovill version 1.0.4 [23 (link)] and annotated using Prokka software [24 (link)]. Single nucleotide polymorphism (SNP) analysis was performed using Snippy [25 (link)]. The online tool DAVID [26 (link)] was used to annotate SNP genes according to biological function and cellular components via Gene Ontology analysis [27 (link)]. The genome of the E. coli strains were submitted to GenBank under accession number PRJNA907472.