Vibriophage VpV262

Host: Vibrio parahaemolyticus - subject to pathogenic conversion, causing an pandemic of shellfish poisoning.

Isolation: by Andre Comeau and Curtis Suttle by ultraconcentration of plankton from 200 L of surface water from the Strait of Georgia, British Columbia.

Morphological examination: short tailed Podovirus, ~75 nm head, ~ 40 kb genome expected.

Objective: Sequence and determine type of phage. I.e., is it temperate or lytic, and what is the closest characterized prototype.

Special methodology used:

• Due to short supply of DNA, ordinary shotgun cloning and sequencing from viral template was not workable.
• Used shotgun cloning of restriction fragments, specialized software to decompose chimeric clones, comparative methods to hypothesize contig order, and PCR to raise templates for closing gaps.

• 46,016 bp genome with 138 bp terminal repeats and blunt ends.
• Two converging transcription units.
• One tRNA.
• One apparent moron.
• 63 open reading frames.
• Genes identified as to Probable function:
• DNA polymerase with 3' exo (distant)
• 5' exo (distant)
• ParB (chromosome partitioning gene - distant)
• HNH nuclease (a mobile gene)
• 6 genes matching marine Roseophage SIO1, none of which had either functional assignment or any identified homologues.

• We will have to do better at gene identification that what just a plain blast search can tell, or else we can not even make a statement about what kind of phage this might be.