Annotated genomes (gff files)

PacBio contigs were polished by mapping of Illumina reads using the Burrows-Wheeler Aligner v0.7.12-r1039 and identification and correction of sequence deviations by VarScan v2.3.6, applying the “mpileup2cns” command with minimum coverage of 10, at least six supporting reads, minimum read base quality of 20, a variant allele frequency threshold of 0.8, and a p-value of 0.01. If necessary, the resulting chromosomal and extrachromosomal contigs were manually circularized and shifted to dnaA as start point. For automated annotation, we used Prokka v1.14.6.