Genomic DNA Extraction and Sequencing

The genomic DNA of the isolates was extracted using TIANamp Bacteria DNA Kit (Beijing Tiangen, China) and then sequenced using Illumina NovaSeq PE150 at Beijing Novogene Bioinformatics Technology Co., Ltd. Sequencing libraries of ∼ 350 bp were prepared using NEBNext® Ultra™ DNA Library Prep Kits and analysed for size distribution using an Agilent 2100 Bioanalyzer and quantified using real-time polymerase chain reaction. SOAP denovo [23 (link)] was used to assemble paired reads. All of the genomic sequences are available at the National Center for Biotechnology Information (NCBI; accession nos. SAMN21988700, SAMN22062944-49). Further, as VFBJ05 and VFBJ07 were found to own transposon islands, the extracted DNA of them were further subjected to 250-bp paired-end whole-genome sequencing with 150× coverage using the Nanopore sequencer. The filtered subreads were assembled using Canu v1.5 [24 (link)], and then Circlator v1.5.5 (https://github.com/sanger-pathogens/circlator) was used to cyclise the assembled genomes. Coding gene prediction was performed using Prodigal v2.6.3 [25 (link)]. Genome annotation was performed using the RAST server (https://rast.nmpdr.org/rast.cgi). The whole-genome sequences of VFBJ05 and VFBJ07 are available at the NCBI (accession nos. SAMN35555507 and SAMN35555508).