Salmonella Phage Genomic Extraction and Sequencing

Genomic DNA from the Salmonella phages was extracted using the Wizard DNA Clean-Up system (A7280; Promega, Madison, WI, USA) following the modified Promega Wizard method, as described by the Center for Phage Technology, Texas A&M University, USA [32 (link)]. Extracted DNA was purified by ethanol precipitation [33 ] and whole-genome sequencing (WGS) was performed on an Illumina MiSeq platform (Illumina, San Diego, CA, USA) with 300 bp paired-end libraries and 30× coverage. Raw sequence reads were assembled using the A5 pipeline [34 (link)] and genome annotation was completed using the Bacterial and Viral Bioinformatics Resource Center (formerly PATRIC) [35 (link),36 (link)]. Annotations were manually curated and the coding sequences (CDSs) were used to interrogate the NCBI database using BLASTP (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins (accessed on 6 January 2024)) [37 (link)]. An HHpred search of the Pfams database was used to identify conserved protein motifs [38 (link)]. To assign a protein to a gene sequence, at least 90% identity was sought in BLASTP searches for protein motifs [39 (link)]. Based on the presence or absence of a gene encoding integrase, phages were putatively classified as temperate or virulent, respectively [26 (link)].