Phage genome sequencing and analysis

Phage DNA was extracted using the Phage Genome DNA Quick Extraction Kit (Zhuangmeng International Biology Gene Technology Co., Ltd). DNA concentration was determined using a spectrophotometer (Nanodrop Technologies, USA). The PEC9 genomic DNA was sequenced using an Illumina NovaSeq PE150 sequencer and reads were assembled into a whole genome using SOAPdenovov 2.04 software and GapCloserv1.12. High-quality paired-end reads were assembled using A5-MiSeq v20160825 (https://arxiv.org/abs/1401.5130) and SPAdes v3.12.0 (http://cab.spbu.ru/files/release3.12.0/manual.html), and the genome sequence was proofread using software MUMmer v3.1 (http://mummer.sourceforge.net/) (Kurtz et al., 2004) and Pilon v1.18 (https://github.com/broadinstitute/pilon) (Walker et al., 2014). Potential open reading frames (ORFs) were predicted using GeneMarkS v4.32 (Besemer et al., 2001). Genome annotation was analyzed using diamond vO.8.36 (http://github.com/bbuchfink/diamond), HHpre (https://toolkit.tuebingen.mpg.de/#/tools/hhpred), BLAST and Conserved Domain Identify of NCBI. The Virulence Factor Database (http://www.mgc.ac.cn/VFs/main.htm) and Comprehensive Antibiotic Resistance Database (https://card.mcmaster.ca/) were queried to retrieve the toxic genes, virulence genes, and antibiotic resistance genes in the phage genome. tRNAscan-SE search program (https://lowelab.ucsc.edu/tRNAscan-SE/) was used to identify putative tRNAs (Lowe and Chan, 2016). A circular representation of the genome of phage PEC9 was generated using BRIG software. Comparisons and phylogenetic analysis of the genome of phage PEC9 with other phages were conducted with the NCBI BLASTN algorithm (http://blast.ncbi.nlm.nih.gov).