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

The resulting alignment allowed us to compare genome architecture across all of the prophages, and revealed that gene order is conserved across phage genomes (Fig. 7a) , suggesting that there is an advantageous order of clusters of related function within the genomes of prophages. To highlight the clusters, we used a modified Smith-Waterman approach, essentially ascribing a single letter to each of the functions and then aligning the genomes based on the order of the functions with a +1 score for a match and no penalty for a mismatch (Fig. 7b) . This shows that the gene order across 1,537 phage genomes is highly conserved, reminiscent of the early-middle-late gene organization of many well characterized phages and eukaryotic viruses (58) (59) (60) . We also visualized the presence of each gene at its location in the genome using a gene density plot (Fig. 8) , which highlights the separation of the genes based on location in the genome. The combined results from these alignments strongly indicate that the mosaicism in phage genomes occurs at the gene-cluster level, and that phage genomes are not comprised of random hybrids of many genomes. Instead, recombination (illegitimate or otherwise) appears to be constrained to result in a highly conserved gene order where the early genes, including those encoding entry and DNA replication functions, precede those encoding packaging functions, which in turn precede tail formation and host lysis functions.