Complete Genome Sequence of Croceibacter Bacteriophage P2559S

Abstract

Croceibacter atlanticus HTCC2559^T, a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the family Flavobacteriaceae. Strain HTCC2559^T possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559^T. Many genes predicted in the P2559S genome had their homologs in Bacteroides phages.

GENOME ANNOUNCEMENT

Croceibacter atlanticus HTCC2559^T is a marine bacterium isolated from the western Sargasso Sea at a depth of 250 m by using dilution-to-extinction high-throughput culturing (2, 3). This bacterium was shown to be phylogenetically unique in the 16S rRNA gene-based phylogeny. The highest 16S rRNA gene sequence similarity to other validly published species was only 90.6%, which was recorded for Leeuwenhoekiella palythoae (8). Based on the results of polyphasic taxonomy, this bacterium was established as the type species of the genus Croceibacter in the family Flavobacteriaceae, an abundant marine bacterial group well-known for interaction with phytoplankton (2, 4, 6). The genome sequence of C. atlanticus HTCC2559^T (10) was shown to encode a protease showing algicidal activity as well as many proteins related to degradation of macromolecules such as alginate (12). Considering that strain HTCC2559^T showed several characteristics hinting at the interaction with marine primary producers, it would be interesting to isolate and characterize bacteriophages infecting this bacterium, since phages could have influences on the gene transfer and physiology of their hosts. Currently, only a few genome sequences of bacteriophages infecting marine members of the family Flavobacteriaceae are publicly available; therefore, genome information of bacteriophages infecting members of the family would help interpret marine viral metagenome data more thoroughly. Here we announce the genome sequence of bacteriophage P2559S, which lytically infects C. atlanticus HTCC2559^T.

Bacteriophage P2559S was isolated from a surface seawater sample collected off the southern coast of the Korean Peninsula. P2559S had an isometric head and a long noncontractile tail and carried double-stranded DNA, suggesting that the phage belongs to the family Siphoviridae.

A DNA sample for genome sequencing was extracted from phage particles purified by CsCl gradient ultracentrifugation. Genome sequencing was performed by shotgun pyrosequencing. Assembly by gsAssembler (version 2.3) resulted in a single linear contig, which was subsequently circularized by sequencing of PCR products amplified using primers targeting both ends of the contig. Gene prediction and annotation of the genome sequence was carried out using the RAST server (1), the results of which were examined and complemented by BLASTP analysis and RPS-BLAST searches against Pfam and CDD (7, 11).

The genome sequence of P2559S had a length of 44,988 bp with a G+C content of 41.9 mol%, a slightly higher value than that of its host (33.9%) (10). Sixty-eight open reading frames (ORFs) were predicted in the genome. Functional annotation of ORFs showed that the genome contained genes for a terminase-like family protein, tail protein, two capsid proteins, tail-length tape measure protein, N-acetylmuramoyl-l-alanine amidase, RNase H, DNA polymerase III epsilon-subunit, single-stranded DNA binding protein, and S-adenosylmethionine decarboxylase. In preliminary comparative analysis, the genome was revealed to have many genes in common with Bacteroides fragilis phages B124-14 and ATCC 51477-B1 (5, 9). Among 37 predicted proteins that showed E values of less than 10⁻⁵ with their respective best BLASTP matches, 17 proteins had their best matches in the genomes of the two Bacteroides phages listed above.

Nucleotide sequence accession number.

The complete genome sequence of P2559S was deposited in GenBank under accession number JQ867099.