Probing Viral Dark Matter: Comparative Genomics of Atypical Bacillus Phage YungSlug

<i>Bacillus</i> phage YungSlug is a novel phage with a genome that has limited homology to known viruses. To better understand this unique phage, we searched for close relatives of YungSlug using traditional comparative genomics approaches and a broad search of a large protein database. YungSlug shares only 9% genome alignment with Bacillus phage Nachito, its closest relative, and less than 1% with others in its subfamily. A search for homologs in the NCBI nr database was dominated by low percent identity homologs from viral, bacteria, and environmental sources, returning matches for only 50% of the predicted proteins in YungSlug's genome. Additionally, a set of 21 conserved proteins was identified that may define a core gene set for the <i>Spounavirinae</i> subfamily of <i>Herelleviridae</i>. These findings highlight the diversity of phages infecting <i>Bacillus</i> and highlight gaps in our knowledge of the <i>Bacillus</i>-infecting phage community.