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.

使用Burrows-Wheeler比对工具（Burrows-Wheeler Aligner）v0.7.12-r1039对Illumina测序读段进行比对，并借助VarScan v2.3.6软件识别并修正序列偏差，采用"mpileup2cns"命令，设置最低覆盖度为10、至少6条支持读段、最低读段碱基质量值为20、变异等位基因频率阈值为0.8以及p值为0.01，以完成PacBio重叠群（contigs）的抛光校正。若有必要，对所得染色体型及染色体外型重叠群进行手动环化，并将起始位点调整至dnaA。自动化基因组注释采用Prokka v1.14.6软件完成。