Draft Genome Sequences of Porphyromonas crevioricanis JCM 15906^T and Porphyromonas cansulci JCM 13913^T Isolated from a Canine Oral Cavity

Abstract

Here, we report the draft genome sequences of Porphyromonas crevioricanis JCM 15906^T and Porphyromonas cansulci JCM 13913^T, which were isolated from a canine oral cavity and were recently united under the single species P. crevioricanis. These two genome sequences are very similar, and yet a high degree of genome rearrangements is observed.

GENOME ANNOUNCEMENT

Porphyromonas crevioricanis (1) and Porphyromonas cansulci (2) have been isolated from canine oral cavities. P. crevioricanis is one of the predominant bacterial species in subgingival plaque in dogs (3). It has been reported that P. crevioricanis strain JCM 15906^T shows a very high hsp60 gene sequence similarity (100%) with that of P. cansulci JCM 13913^T, as well as a very high 16S rRNA gene sequence similarity (99.9%) (4). Recently, P. crevioricanis and P. cansulci were found to be a single species, P. crevioricanis, based on the relatedness of their DNA (>91%) (5). Therefore, the genome sequences of two strains are expected to provide new insights into this species concept.

Chromosomal DNA was extracted from P. crevioricanis JCM 15906^T and P. cansulci JCM 13913^T using a Genomic-tip 100/G (Qiagen). Whole-genome sequencing was performed using an Illumina genome analyzer IIx, which produced paired-end reads of 101 bp with an insert size of 500 bp. De novo assemblies were performed using Velvet v1.1.02 (6), with parameters optimized by the VelvetOptimiser (http://www.vicbioinformatics.com/software.velvetoptimiser.shtml), resulting in 118 contigs with an N₅₀ of 49,631 bp for P. crevioricanis JCM 15906^T, comprising 2,044,812 bp, with an average G+C content of 45.3%, and 89 contigs with an N₅₀ of 69,079 bp for P. cansulci JCM 13913^T, comprising 2,108,435 bp with an average G+C content of 45.4%. The draft genomes were annotated by the Rapid Annotations using Subsystems Technology (RAST) sever (7) using Glimmer3 as a gene finder (8). The P. crevioricanis JCM 15906^T genome contains 2,086 protein-coding sequences (CDSs), a gene density of 88.6%, an average coding size of 864 bp, three rRNAs, and 48 tRNA sequences. The P. cansulci JCM 13913^T genome contains 2,180 CDSs, a gene density of 88.2%, an average coding size of 850 bp, three rRNAs, and 51 tRNA sequences. According to the genome BLAST distance phylogeny (GBDP)-based DNA-DNA hybridization (DDH) prediction (9), the pair of P. crevioricanis JCM 15906^T and P. cansulci JCM 13913^T genome sequences showed a 96.5% DDH value calculated by the Genome-to-Genome Distance Calculator (GGDC) web server (GGDC 2.0; http://ggdc.dsmz.de/distcalc2.php). BLAST dot plot analysis comparison in the SEED viewer (http://www.theseed.org) indicated a high degree of genome rearrangements between P. crevioricanis JCM 15906^T and P. cansulci JCM 13913^T genome sequences. P. cansulci JCM 13913^T contains large numbers of conjugative transposon proteins, which are frequently associated with genomic rearrangements. This might have contributed to rearrangement of the genomic structure and led to the diversification of P. crevioricanis. Further genome analyses will improve our understanding of this species.

Nucleotide sequence accession numbers.

The draft genome sequences of P. crevioricanis JCM 15906^T and P. cansulci JCM 13913^T have been deposited in DDBJ/EMBL/GenBank under the accession no. BAOU00000000 and BAOV00000000.