Abstract
Scardovia inopinata JCM 12537T was isolated from human dental caries. Here, we report the complete genome sequence of this organism. This paper is the first report to demonstrate the fully sequenced and completely annotated genome of an S. inopinata strain.
GENOME ANNOUNCEMENT
Scardovia inopinata JCM 12537T (=DSM 10107T) was originally isolated as Bifidobacterium inopinatum from human dental caries (1) and then was renamed S. inopinata (2). S. inopinata is classified under the family Bifidobacteriaceae. This species is not only isolated from human dental caries and plaque (3, 4) but is also found in the human hypochlorhydric stomach (5).
We determined the complete genome sequence of S. inopinata JCM 12537T using the whole-genome shotgun strategy using Sanger sequencing (ABI 3730xl sequencers). We constructed small-insert (2-kb) and large-insert (10-kb) genomic DNA libraries and generated 26,880 sequence reads (10.7-fold coverage) for S. inopinata JCM 12537T from both ends of the genomic clones. The data were assembled with the Phred-Phrap-Consed program. Gap closing and resequencing of low-quality regions were conducted by Sanger sequencing to obtain the high-quality finished sequence. The overall accuracy of the finished sequence was estimated to have an error rate of <1 per 10,000 bases (Phrap score, ≥40). An initial set of predicted protein-coding genes was identified using Glimmer 3.0 (6). Genes consisting of <120 bp and those containing overlaps were eliminated. The tRNA genes were predicted by the tRNAscan-SE (7), and the rRNA genes were detected by a BLASTn search using known Scardovia rRNA sequences as queries.
The genome sequence of S. inopinata JCM 12537T consists of a circular chromosome of 1,797,862 bp, with no plasmid. The genome size is smaller than those of the Bifidobacterium species, whose genomes range in size from 1.9 to 2.8 Mbp (8). JCM 12537T contains a clustered regularly interspaced short palindromic repeat (CRISPR) (9) region (positions 468740 to 470632), and three CRISPR-associated genes (SCIP_0361 to SCIP_0363) were encoded upstream of the CRISPR region. The chromosome contains 1,445 predicted protein-coding genes. S. inopinata JCM 12537T is related to Parascardovia denticolens in the phylogenetic tree of the family Bifidobacteriaceae (10). Next, we compared the genome of JCM 12537T with that of P. denticolens JCM 12538T (1,890,857 bp) (GenBank accession no. AP012333). Of the 1,445 protein-coding genes, 1,070 (74%) were conserved in the two strains. The genome information of this species will be useful for further studies of its physiology, taxonomy, clinical aspects, and ecology.
Nucleotide sequence accession number.
The sequence data for the genome have been deposited in DDBJ/GenBank/EMBL under the accession no. AP012334.
ACKNOWLEDGMENTS
This research was partly supported by “CREST” (research projects pursued by research teams led by research directors) to K.H., K.O., and H.M., and by grants-in-aid for scientific research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT) (grant 24593135 to J.-I.H.).
Footnotes
Citation Oshima K, Hayashi J-I, Toh H, Nakano A, Omori E, Hattori Y, Morita H, Honda K, Hattori M. 2015. Complete genome sequence of Scardovia inopinata JCM 12537T, isolated from human dental caries. Genome Announc 3(3):e00481-15. doi:10.1128/genomeA.00481-15.
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