# A Novel Benthic Phage Infecting _Shewanella_ with Strong Replication Ability
## 3 Results and Discussion
### Genomic Features of the Phage S0112  
The phage S0112 genome consisted of 62,286 bp of linear ds DNA, with the average G+C content of 44.7%, which is lower than that of its host (51.2%) [20]. PhageTerm analysis showed that the DNA termini and packaging mechanisms of phage S0112 is similar with that of T5-like phages. No tRNA genes were found in the phage genome. Furthermore, the genome of phage S0112 was searched against viral spacer database of IMG/VR and spacers within CRISPR of its host. The result showed no match between phage S0112 and viral spacers sequences within CRISPR. The phage genome was predicted to encode 102 putative open reading frames (ORFs), of which only 42 ORFs were assigned putative functions based on their amino acid sequence homology to known proteins. About 59% of the ORFs (60 ORFs) are functionally unknown, among which 21 ORFs were annotated as hypothetical proteins and 39 ORFs had no any homology with protein databases (Table S3). Among the 42 ORFs with known functions, eight ORFs shared similarities with that of _Vibrio_ phage VpKK5, which is also a siphovirus isolated from the marine sediments [18], with percent identities of 42-59%; six ORFs share similarities with the _Pantoe_ phage vB_PagS_Vid5 and _Pseudomonas_ phage MP1412; and eight ORFs shared low identity with _Alphaproteobacteria_ phage JI001, Roseophage RDJL \(\phi\) 1 and _Burkholderia_ phage BeepGonn. All the genes with homology to S0112 are from siphoviruses. So far, nine _Shewanella_ phage genomes were reported [12; 13; 14; 15]. These phages vary significantly in phage size, GC content, protein amount, and isolation sources (Table 3). Multiple genome alignments of the nine _Shewanella_ phages and phage S0112 showed that the genome of phage S0112 has a very small amount of similarity with others [32] (Figure 5). Among phage S0112 genome, only three ORFs of phage S0112 show certain similarities with other _Shewanella_ phages, including S0112_005 (DNA/RNA helicase), S0112_018 (primase/helicase), and S0112_053 (hypothetical protein). The encoded proteins of phage S0112 can be divided into four functional modules: DNA packaging module, structure/morphogenesis module, DNA replication/recombination/metabolism module, and queuosine biosynthesis module (Figure 6). The DNA packaging module mainly includes the gene product S0112_063 (terminase small subunit) and S0112_064 (terminase large subunit, sharing 49.3% amino acid identity with the corresponding proteins of _Fodinicurate sedimini_s). It is reported that terminase generally consists of one larger submit and one small submit. The role of the terminase small submit is to specifically recognize the packaging initiation site (_cos_ or _pac_) and helps assemble a holozyme complex with a larger submit which can cleave genomic DNA at special site, to ensure the whole genome into preassembled empty capsids, using its endonuclease and ATPase activities [43]. Figure 5: Multiple genome alignments of the whole genomes of all _Shewanella_ phages, using Mauve algorithm. The _Shewanella_ phages in the analysis are isolated from different environments, including Baltic Sea ice, seawater, sewage, waste effluents from fish market, and coastal sediments. Colored boxes indicate homologous DNA regions between genomes without genomic rearrangements. Genomic similarity is represented by the height of the bars, which corresponds to the average level of conservation in that region of the genome sequence. Completely white regions represent fragments that were not aligned or contained sequence elements specific to a particular genome.