a. Structural comparisons of the PVL phages. Structures of phi7401PVL and phiSa2mw are illustrated based on the nucleotide sequences deposited in databases DDBJ/EMBL/GenBank under accession nos. BA000033 for phiSa2mw and AP012341 for phi7401PVL. Red arrowhead indicates the location of attP. Black bars indicate the locus of amplified DNA fragments using 5 sets of primers. Green bars indicate the locus of amplified DNA fragment identifying the carriage of gene linkages in phi7401PVL. ORFs are colored as follows: orange, ORFs related to lysogeny; red, a ORF in DNA replication/recombination region with assigned functions; bright green, ORFs related to capsid formation; yellowish orange, ORFs related to head formation; yellowish green, ORFs related to tail formation; blue, ORFs related to cell lysis; black, lukS-PV and lukF-PV. The locations of the primers are indicated in lines flanked by arrow heads. Nucleotide sequences of the primers are listed in Additional file 2: Table S2. b. Comparisons of the two phage genomes with a dot plot analysis. The genome sequence of phi7401PVL was compared to those of phiPVL (group 1 cos-site Siphoviridae), phiSa2mw (group 2 cos-site Siphoviridae), and phiN315 (group 3 cos-site Siphoviridae) using a specialized BLAST at NIBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi webcite). Ordinate indicates the genome phi7401PVL. Abscissa indicates the genomes of three phages, phiPVL, phiSa2mw, and phiN315, in dot plots A, B, and C, respectively.
Mariem et al. BMC Microbiology 2013 13:2 doi:10.1186/1471-2180-13-2