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Draft genome sequence of Streptococcus constellatus KCOM 1039 isolated from human postoperative maxillary cyst lesion
Korean J. Microbiol 2019;55(1):67-68
Published online March 31, 2019
© 2019 The Microbiological Society of Korea.

Soon-Nang Park1,†, Yun Kyong Lim1,†, Seong-Chul Hong2, Ja Young Shin3, Hanseong Roh3, and Joong-Ki Kook1,*

1Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju 61452, Republic of Korea,
2School of Dentistry, Chosun University, Gwangju 61452, Republic of Korea,
3Macrogen Inc., Seoul 08511, Republic of Korea
Correspondence to: E-mail: jkkook@chosun.ac.kr; Tel.: +82-62-230-6877; Fax: +82-62-236-2734
Received December 24, 2018; Revised December 30, 2018; Accepted January 16, 2019.
Abstract

Streptococcus constellatus is Gram-stain-positive, facultative anaerobic, and non-spore forming coccus. It is a member of normal flora of human oral cavity. S. constellatus KCOM 1039 was isolated from human postoperative maxillary cyst lesion. In this report, we present the draft genome sequence of S. constellatus KCOM 1039.

Keywords : Streptococcus constellatus, human, postoperative maxillary cyst
Body

Streptococcus constellatus is Gram-stain-positive, facultative anaerobic, and non-spore forming coccus which are round to slightly oval and occur in pairs and short chain (Whiley et al., 1999). It showed beta-hemolytic activity and produced a streptolysin S-like protein (Tabata et al., 2014). The bacterium is primarily inhabits the human oral cavity and is considered to be an opportunistic human pathogen (Tabata et al., 2014). S. constellatus KCOM 1039 (= ChDC B280) was isolated from human periodontitis lesion. In this report, we presented the draft genome sequence of S. constellatus KCOM 1039.

S. constellatus KCOM 1039 was grown in brain heart infusion (BHI, Difco Laboratories) medium in an anaerobic chamber (Model Bactron I) maintained using a gas mixture of 10% H2, 5% CO2, and 85% N2. Genomic DNA of S. constellatus KCOM 1039 was prepared as previously described (Cho et al., 2015).

Genomic DNA of S. constellatus KCOM 1039 was sequenced using the Illumina Hiseq 2000 platform by Macrogen Inc. Three libraries of 350 bp paired-end, 5 kb mate-pair, and 8 kb mate-pair were sequenced which reached coverage of 657.0 ×, 646.2 ×, and 955.7 ×, respectively. The de novo assembly was performed by SPAdes (http://bioinf.spbau.ru/spades) (Bankevich et al., 2012). All gaps among the scaffolds were filled by GapCloser (http://soap.genomics.org.cn/soapdenovo.html) (Luo et al., 2012). Error correction was performed by Pilon (https://github.com/broadinstitute/pilon/wiki) (Walker et al., 2014). Genome annotation was conducted by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm. nih.gov/genome/annotation_prok/) (Tatusova et al., 2016).

The draft genome of S. constellatus KCOM 1039 was composed of 2 contigs; 1,883,587 bp and 2,215 bp in length. The average G+C content of the genome was 38.0%. A total of 1,730 protein-coding sequences, 9 complete rRNA operons (3 5S rRNAs, 3 16S rRNAs, and 3 23 rRNAs), 58 tRNAs, and 3 ncRNAs were identified (Table 1).

Genome features of Streptococcus constellatus KCOM 1039

AttributeValue
Genome size (bp)1,885,802
GC content (%)38.0
No. of contigs2
Total genes1,898
Protein-coding genes1,730
tRNA58
Complete rRNA (5S, 16S, 23S)9 (3,3,3)
ncRNA3
Pseudogene97

In the genome, genes involved in proteinase were identified; putative protease YdcP/YdeA, protease HtpX, ATP-dependent zinc metalloprotease FtsH, putative zinc metalloprotease, Lon protease, rhomboid protease GluP, serine protease Do-like HtrA, and putative zinc protease AlbF. It also contained antibiotic- resistance-related genes; multiple antibiotic resistance protein MarA/MarR, daunorubicin/doxorubicin resistance ATP-binding protein DrrA, putative multidrug resistance ABC transporter ATP-binding/permease protein YheI/YheH, multidrug resistance protein NorM, and tetracycline resistance protein TetM from transposon TnFO1. It also contained biofilm formation-related genes; toxin-antitoxin biofilm protein TabA, putative glycosyltransferase EpsH/EpsJ/CsbB, biofilm regulatory protein A, and D-inositol-3-phosphate glycosyltransferase. It also contained type II secretion system protein F, protein translocase subunit SecA/SecY, and ESAT-6 secretion accessory factor EsaA. The genome also contained the oxidative stress-response genes; glutathione reductase and thioredoxin reductase. Hemolysin A and diphtheria toxin repressor were also found in the genome sequence.

The S. constellatus KCOM 1039 strain was deposited into the Korean Collection for Oral Microbiology.

Nucleotide sequence accession number

This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession QWKV00000000. The version described in this paper is version QWKV00000000.

적 요

Streptococcus constellatus는 그람 염색에 양성을 띄며, 조건혐기성이면서 아포를 생성하지 않는 구균이다. S. constellatus는 사람 구강의 정상 세균 총에 속한다. 수술후 상악낭종 병소에서 S. constellatus KCOM 1039 균주가 분리되었다. 여기에서 S. constellatus KCOM 1039 균주의 유전체 염기서열을 결정하여 보고한다.

Acknowledgements

This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2018R1A2B5002239).

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March 2019, 55 (1)
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