Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards

Across the most highly represented phyla, there were an average of between 2.7 (Actinobacteria) and 3.8 (Proteobacteria) prophages found per genome. Within phyla there were also differences (although not statistically significant) in the prophage genome content. For example, Sodalis glossinidius, a proteobacterium, had the most prophages at 29, while several phyla (Caldiserica, Deinococcus-Thermus, Dictyoglomi, Elusimicrobia, and Fibrobacteres) had no prophages, Spirochetes had the shortest prophage genomes on average (25,595 bp), and Bacteroidetes had the longest (46,059 bp) (Fig. 3) . Across all of the prophages, the mean and median prophage genome length was 36,804 bp and 32,352 bp, respectively. Shorter prophage genomes may indicate that the phage is no longer viable and is in the process of being degraded or removed from the host's genome (32) . Alternatively, different genome lengths may represent different packaging strategies used by prophages associated with different phyla (33) .