Draft Genome Sequence of Porphyromonas gingivalis Strain 381 Okayama (381OKJP) Stock Culture

We report the draft genome sequence of Porphyromonas gingivalis strain 381 Okayama (381OKJP). The strain, obtained from the Socransky collection, has been used for experimentation since 1987.

Recently, the Progulske-Fox group reported the genome sequence for strain 381, which based on genome cluster analysis and gene order revealed the strain to be closely related to ATCC 33277 (9). Strain 381OKJP, selected for this analysis, a generous gift from Sigmund S. Socransky (ca. 1987), was originally deposited in the culture collection at the Department of Oral Microbiology at the Okayama University Dental School (10). Strain 381OKJP (fimA genotype V, mfa1 genotype II [53-kDa Mfa1], ISPg4) is phenotypically distinct from the previously reported strain 381 (fimA genotype I, mfa1 genotype I [67/75-kDa Mfa1], no ISPg4). This study confirms the worldwide distribution of variable 381 strains. The genome sequence of 381OKJP will provide for strain comparisons and analyses of genome rearrangements and information related to 381OKJP-specific phenotypic characteristics.
P. gingivalis 381OKJP was cultured in duplicate at 37°C in Gifu anaerobic medium (GAM) broth, modified (Nissui Pharmaceutical Co., Japan), containing 10 g/ml hemin and 5 g/ml vitamin K 1 under anaerobic conditions (Ͻ0.1% oxygen, Ͼ15% CO 2 ) in a GasPak 100 jar (Becton, Dickinson, USA) with an AnaeroPack-Anaero generator (Mitsubishi Gas Chemical Company, Japan). Cells were collected by centrifugation and washed twice with Gibco phosphate-buffered saline (Thermo Fisher Scientific, Japan). Genomic DNA from two independent samples was extracted and purified using a NucleoSpin tissue kit (TaKaRa Bio, Japan), according to the manufacturer's instructions.
Genomic libraries containing 150-to 550-bp inserts were constructed using the Kapa HyperPlus library kit. The duplicate libraries were independently paired-end sequenced using the Illumina MiSeq platform, and run statistics were determined using CLC Genomics Workbench (version 9.0.1; CLC Bio) ( Table 1). The A5-miseq assembly pipeline was used to automate read trimming and adapter removal from the pairedend FASTQ data and to assemble the reads into contigs (version 20160826) (11,12). QUAST was used to check the quality of each assembly and compare contigs to previously published genomes available from the NCBI (13). The independent genomes were aligned against each other with progressiveMauve, and the Mauve Contig Mover was used iteratively to infer contig order (version 2.4.0 [14]). The final draft genome reported here contains 1,296,214 reads (N 50 , 44,243 bp), producing 128 contigs with 75.89-fold coverage for error-corrected bases.
The final assembly resulted in 2,331,065 bp, with a GC content of 48.4%, consistent with NBCI-deposited P. gingivalis genomes. To confirm taxonomic classification and identify lateral gene transfer events, all scaffolds were aligned to the nonredundant-microbial_20140513 reference database using the LAST algorithm with the Taxator toolkit (v1.3.3e [15]; v938 [16]). Taxonomic classification was supported by 1,720,921 bp, and all assigned sample sequence segments were homologous to those of P. gingivalis. Annotation was performed by the NCBI using the Prokaryotic Genome Annotation Pipeline (PGAP; best-placed reference protein, version 4.2 [17]).
Data availability. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number QPGS00000000. The version described in this paper is version QPGS01000000. The raw reads have been deposited at the NCBI/SRA under BioProject number PRJNA475798.