Complete Genome Sequence of Bacteriophage phiAS7, a T7-Like Virus That Infects Aeromonas salmonicida subsp. salmonicida

Abstract

To date, a number of Myoviridae bacteriophages that infect Aeromonadaceae have been identified and characterized. However, the genome sequences of Aeromonas phages that not belong to the Myoviridae have not been investigated yet. Herein, we report the complete genome sequence of Aeromonas phage phiAS7, which belongs to the Podoviridae and infects Aeromonas salmonicida subsp. salmonicida.

GENOME ANNOUNCEMENT

Aeromonas salmonicida subsp. salmonicida, which belongs to the family Aeromonadaceae in the Gammaproteobacteria group, is the causative agent of furunculosis in salmonid cultures worldwide (7). To date, a number of phages that infect Aeromonadaceae have been reported (1), and most of them are classified into the Myoviridae family as P1-, P2-, and T4-like viruses based on extensive genomic characterizations (3, 5, 6). However, the genome sequences of Aeromonas phages that belong to the Podoviridae have not been investigated previously.

Aeromonas phage phiAS7 was isolated from a sediment sample from a fish farm using the host strain A. salmonicida subsp. salmonicida ATCC 33658. As might be predicted (9), phiAS7 was extremely host specific, with cross-infectivity observed with only one of the possible A. salmonicida subsp. salmonicida strains.

Genomic DNA was extracted as previously described (8) and sequenced using standard shotgun sequencing reagents and a 454 GS-FLX Titanium sequencing system (Roche) by Macrogen in Korea (approximately 100× coverage). The full-length genome sequence was obtained by sequence assembly using SeqMan II sequence analysis software (DNASTAR). The putative open reading frames (ORFs) were predicted using Glimmer 3.02 (2) and GeneMark.hmm (4) software, and the putative functions of the ORFs were determined by BLASTP and InterProScan (11) searches.

The double-stranded DNA genome of phiAS7 was 41,572 bp in length with a G+C composition of 56.9%, and it possessed 147 bp of terminal repeats at its genomic termini. A total of 51 ORFs encoding more than 45 amino acid residues were identified, and the total lengths and capacities of all of the ORFs were 92.5% (38,463 bp) and 92.2% (38,317 bp), respectively, according to Glimmer and GeneMark. All of the predicted ORFs (except the orf21 gene) were positioned on one of the two DNA strands. Nineteen of the ORFs showed no homology to proteins from the GenBank database, whereas the other 32 ORFs code for proteins with some homology (≤66%) to known phage or phage-related bacterial proteins.

Bioinformatic analyses led to the assignment of putative functions to 22 ORFs, and the identified ORFs formed at least three genomic clusters that are involved in viral DNA metabolism (the orf2, orf4, orf6, orf7, orf27, orf28, orf43, orf45, orf46, orf48 and orf50 genes), morphogenesis (the orf24, orf30, orf34, orf35, orf36, orf37, orf38 and orf41 genes), and lysis (the orf25, orf29 and orf31 genes). Most ORFs encoding viral DNA metabolism-associated genes were homologous to those of T7 or T7-like phages, and several viral morphogenesis-related genes were highly similar to those of the Caulobacter phage Cd1, which is classified as a T7-like virus (3). Therefore, phiAS7 might use a viral DNA metabolism and morphogenesis system similar to that of T7 or T7-like phages. In addition, the orf25 and orf29 gene products in phiAS7 were, respectively, predicted to be lysozyme (similar to phage lysozyme domain [PF00959]) and holin (similar to phage holin 6 domain [PF10746]), thus indicating that this phage might use a dual-lysis system (10) during its lytic cycle. The genome sequencing of phiAS7 revealed that this phage could be classified as a new member of the T7-like phage family, and this sequence information will advance our understanding of the biodiversity of Aeromonas phages.

Nucleotide sequence accession number.

The genome sequence of the Aeromonas phage phiAS7 was deposited in GenBank under accession number JN651747.