Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated from Biphenyl-Contaminated Soil in Japan.

Pseudomonas abietaniphila KF717 utilizes biphenyl as a sole source of carbon and energy and degrades polychlorinated biphenyls (PCBs). We report here the 6,930,016-bp genome sequence of this strain, which contains 6,323 predicted coding sequences (CDSs), including the biphenyl-utilizing bph gene cluster.

GENOME ANNOUNCEMENT

Polychlorinated biphenyls (PCBs) have been recognized worldwide as serious environmental pollutants. Pseudomonas abietaniphila strain KF717 was isolated from biphenyl-contaminated soil in Kitakyushu, Japan, as a PCB degrader that utilizes biphenyl as a sole source of carbon and energy (1, 2). Whole-genome shotgun sequencing on strain KF717 was performed by the National Institute of Technology and Evaluation (NITE) by using a combination of shotgun sequencing with a 454 GS FLX+ system (Roche) and paired-end sequencing using a MiSeq sequencing system (Illumina). The Newbler software package (version 2.6; Roche) was used for the genome assembly. The draft genome size is 6,930,016 bp and contains 97 contigs, with an average contig length of 71.4 kb, a median coverage depth of 92-fold, and an average G+C content of 59.4 mol%.

The genome sequence of strain KF717 was uploaded to the RAST server (http://rast.nmpdr.org) to predict the open reading frames (ORFs), tRNAs, and rRNAs (3). Rapid genome annotation using the RAST annotation server revealed 6,323 coding sequences (CDSs), 60 tRNA sequences, and 4 rRNA sequences. The coding sequences were classified into 4,026 subsystems, with the most abundant being systems involved in the metabolism of amino acid derivatives (n = 567 CDSs) and carbohydrates (n = 509), the production of cofactors, vitamins, prosthetic groups, and pigments (n = 301), protein metabolism (n = 290), the stress response (n = 227), and the production of cell wall and capsule (n = 212). A comparison of P. abietaniphila KF717 with other Pseudomonas strains within the RAST database identified Pseudomonas syringae pv. actinidiae CFBP 7286 (RAST server genome ID 1094176.3) as its closest neighbor, with a score of 494, followed by P. syringae pv. phaseolicola 1448A (genome ID 264730.3), with a score of 481. Pseudomonas fluorescens Q8r1-96 (genome ID 1038923.3) was the sixth closest neighbor, with a score of 459. P. syringae is known as a pathogen of many plant species (4), and P. fluorescens Q8r1-96 was identified as a plant growth-promoting rhizobacterium (PGPR) (5).

The comparison of the functional annotation was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) (6). Strain KF717 was found to possess the ring-hydroxylating dioxygenase, the alpha and beta subunits of biphenyl degradation, whole-benzoate degradation via the hydroxylation pathway, and phenol hydroxylase components of the phenol degradation pathway.

Nucleotide sequence accession numbers.

The whole-genome sequence of P. abietaniphila KF717 has been deposited in DDBJ/EMBL/GenBank under the accession numbers BBQR01000001 to BBQR01000097.