Genome Sequencing and Annotation of Strain Cp2

Concentration and purity of the genomic DNA were quantified with TBS-380 Mini-Fluorometer (Turner BioSystems) and NanoDrop 2500, respectively. The genome of strain Cp2 was sequenced by Shanghai Majorbio Bio-Pharm Technology Co., Ltd., Shanghai, China using Illumina HiSeq and PacBio methods. After sequencing, clean reads were obtained from the raw reads by removing adaptor sequences, reads containing low-quality reads and poly-N. The resulting clean reads were used for scaffolding by SOAPdenovo software. High-quality PacBio long reads were assembled by using Canu (Koren et al., 2017 (link)). After assembly, circular chromosomes and plasmids with gapless were finally generated and drawn using the CGView program (Stothard and Wishart, 2005 (link)). Prediction of genes for protein coding sequences (CDSs), transfer RNA (tRNA), and ribosomal RNA (rRNA) was performed with Glimmer, GeneMarks, tRNAscan-SE, and Barrnap software, respectively (Besemer et al., 2001 (link); Seemann, 2013 ; Lowe and Chan, 2016 (link)). In addition, each predicted CDS was annotated through the Clusters of Orthologous Genes (COG) database by BLAST (Tatusov et al., 2003 (link)). Genes associated with virulence were identified in the Virulence Factors Database (VFDB) and Pathogen-Host Interaction Database (PHI-base) (Chen et al., 2005 (link); Winnenburg et al., 2006 (link)).