Fig 5.

Physical ends of the phage genome. (A) The phage genomic DNA was treated with Bal31 for 0, 30, and 60 min and thereafter digested with KpnI. The 5.7- and 2.7-kb KpnI fragments that disappear in the 30- and 60-min samples are indicated. M lanes, molecular mass markers. (B) Snapshots of sequencing reads using whole-phage genome or the isolated 6-kb SphI fragment as the template, demonstrating the end of the template. In the whole genome read, the sequence intensity drops to half due to the end of the template in the left end of the genome, while the primers that started the reads from the redundant right end of the genome continue further. (C) Strategy to detect the circular form of the phage genome by Southern blotting. A probe covering nt 258,737 to 259,767 would hybridize only to the 15.7-kb KpnI fragment if the replicating form of the genome was circular but to 5.7- and 15.7-kb KpnI fragments if it was linear.