search for




 

Draft genome sequence of Pelagicola sp. DSW4-44 isolated from seawater
Korean J. Microbiol 2019;55(3):283-285
Published online September 30, 2019
© 2019 The Microbiological Society of Korea.

Ji-Sung Oh and Dong-Hyun Roh*

Department of Microbiology, Chungbuk National University, Cheongju 28644, Republic of Korea
Correspondence to: *E-mail: dhroh@chungbuk.ac.kr; Tel.: +82-43-261-3368; Fax: +82-43-264-9600
Received August 12, 2019; Accepted August 18, 2019.
Abstract
The draft genome sequencing for Pelagicola sp. DSW4-44 (= KCTC 62762 = KCCM 43261), isolated from deep seawater of East Sea in Korea, was performed using Illumina HiSeq platform. As a result, the draft genome was comprised of a total length of approximately 4.85 Mbp with G + C content of 54.3%, and included a total of 4,566 protein-coding genes, 3 rRNA genes, 48 tRNA genes, 3 non-coding RNA genes, and 67 pseudo genes. In the draft genome, the strain DSW4-44 contained genes involved in the nitrogen metabolism of dissimilatory nitrate reduction to ammonium (DNRA) and denitrification, which were not found other strains in the genus Pelagicola.
Keywords : Pelagicola sp. DSW4-44, draft genome sequence, Illumina HiSeq
Body

The family Rhodobacteraceae, belong to the order Rhodobacterales of the class Alphaproteobacteria, currently comprises 161 genera (List of Prokaryotic Names with Standing in Nomenclature; http://www.bacterio.net). Members of the family Rhodobacteraceae are known to inhabit in various marine environments and participate in biogeochemical cycling of sulfur and carbon, and symbiosis with micro-and macro-organisms (Pujalte et al., 2014). The genus Pelagicola, belong to the family Rhodobacteraceae, was first proposed by Kim et al. (2008), and includes 2 type species: P. litoralis (Kim et al., 2008) and P. litorisediminis (Park et al., 2013). To date, a total of 3 genomes of the genus Pelagicola were sequenced and annotated, and Pelagicola sp. LXJ1103 was reported that it contained genes for sulfur metabolism such as sulfate transporter, sulfate permease, sulfate adenylyltransferase, and phosphoadenosine phosphosulfate reductase (Zhao et al., 2018). In this report, we describe the draft genome sequence and annotation of Pelagicola sp. DSW4-44 isolated from East Sea of Korea.

The Pelagicola sp. DSW4-44 was isolated from deep seawater (depth of 200~500 m, 38° 21’ 25” N 128° 35’ 30” E), using a standard dilution plating method on marine agar 2216 (MA; Difco). Among the type strains of EzBioCloud server (https://www.ezbiocloud.net/), Pelagicola litoralis CL-ES2T had the closest 16S rRNA similarity (96.5%) to strain DSW4-44. For the sequencing of the draft genome, the cells were incubated at 25°C in marine broth 2216 (MB; Difco) for 5 days and the genomic DNA was extracted using MagAttract® HMW DNA kit (Qiagen). The sequencing of the draft genome was performed on the Illumina Hiseq platform by Macrogen Inc. Quality checking of sequencing data was performed by FastQC (version 0.11.5) and the de novo assembly was performed by SPAdes (version 3.10.0). The potential contamination of the draft genome was assessed using ContEst16S (Lee et al., 2017). Genome annotation and functional characterization of genome were conducted by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) (Tatusova et al., 2016) and BlastKOALA (Kanehisa et al., 2016).

The draft genome of Pelagicola sp. DSW4-44 consisted of 23 contigs with a total length of 4,852,500 bp and N50 size of 413,599 bp. The sequencing depth of coverage was 157.4 X and the genomic DNA G + C content was 54.3 mol%. A total of 4,566 protein coding genes, 3 rRNA genes (each 1 for 5S rRNA, 16S rRNA, and 23S rRNA), 48 tRNA genes, 3 non-coding RNA, and 67 pseudo genes were predicted (Table 1).

Genome features of Pelagicola sp. DSW4-44

Genome features Value
No. of contigs 23
Depth (X) 157.4
Genome size (bp) 4,852,500
G + C content (%) 54.3
Protein-coding genes 4,566
tRNA genes 48
rRNA genes (5S, 16S, 23S) 3 (1, 1, 1)
Non-coding RNA genes 3
Pseudo genes 67


The genome sequence contained genes for sulfur metabolism. L-Cysteine S-thiosulfotransferase soxAX, S-sulfosulfanyl-L-cysteine sulfohydrolase soxB, sulfane dehydrogenase subunit soxC, S-disulfanyl-L-cysteine oxidoreductase soxD and sulfur-oxidizing protein soxYZ, involved in the oxidation of thiosulfate to sulfate by SOX system, were detected. Interestingly, the genome also contained genes for nitrogen metabolism, which were not found other strains in the genus Pelagicola. Periplasmic nitrate reductase napA and cytochrome c-type protein napB, involved in first common step of the dissimilatory nitrate reduction to ammonium (DNRA) and denitrification genes for conversion of nitrate to nitrite, has been identified. For DNRA, nitrite reductase (NADH) large subunit nirB, nitrite reductase (NADH) small subunit nirD, related to second step (respiratory nitrite reduction to ammonium), were detected. Nitrite reductase (NO-forming) / hydroxylamine reductase nirS, nitric oxide reductase subunit B norB, nitric oxide reductase subunit C norC and nitrous-oxide reductase nosZ were detected, which were related to denitrification of nitrate to nitrogen. These genes in the sulfur and nitrogen metabolism in Pelagicola sp. DSW4-44 are thought to play an important role in biogeochemical cycling.

Nucleotide sequence accession numbers

The strain Pelagicola sp. DSW4-44 is available at KCTC 62762 and KCCM 43261. The draft genome sequence is accessible in GenBank under the accession number VAUA 00000000. The version described in this paper is Version VAUA01000000.

적 요

이 연구에서는 Illumina Hiseq platform을 사용하여 동해 심층 해양수로부터 분리된 Pelagicola sp. DSW4-44 (= KCTC 62762 = KCCM 43261)의 초안 유전체 염기서열 해독을 수행하였다. 그 결과, 유전체는 대략 4.85 Mbp의 길이 및 54.3%의 G + C 함량으로 구성되었고, 전체 4,566개의 단백질 암호 유전자, 3개의 rRNA 유전자, 48개의 tRNA 유전자, 3개의 non-coding RNA 유전자 및 67개의 위유전자(pseudo gene)가 확인되었다. 초안 유전체에서 균주 DSW4-44는 Pelagicola 속의 다른 균주에서 발견되지 않는 이화적 질산염의 암모늄 환원과 탈질화의 질소대사 유전자를 가지고 있었다.

Acknowledgements

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1D1A3B04033871).

References
  1. Kanehisa M, Sato Y, and Morishima K. 2016. BlastKOALA and GhostkOALA:KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol 428, 726-731.
    Pubmed CrossRef
  2. Kim YG, Hwang CY, and Cho BC. 2008. Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea. Int. J. Syst. Evol. Microbiol 58, 2102-2106.
    Pubmed CrossRef
  3. Lee I, Chalita M, Ha SM, Na SI, Yoon SH, and Chun J. 2017. ContEst16S:An algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol 67, 2053-2057.
    Pubmed CrossRef
  4. Park S, Jung YT, and Yoon JH. 2013. Pelagicola litorisediminis sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment. Antonie van Leeuwenhoek 104, 103-110.
    Pubmed CrossRef
  5. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, and Macián MC. 2014. The family Rhodobacteraceae pp. 439-512. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, and Thompson F (eds.) The prokaryotes Alphaproteobacteria and betaproteobacteria, Springer Berlin Heidelberg,.
    CrossRef
  6. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44, 6614-6624.
    Pubmed CrossRef
  7. Zhao D, Li J, Lin S, Liang X, Lin X, and Sun X. 2018. Draft genome sequence of Pelagicola sp. strain LXJ1103, isolated from coastal surface seawater. Microbiol. Resour. Announc 7, -18.
    Pubmed CrossRef


September 2019, 55 (3)
Full Text(PDF) Free

Social Network Service
Services

Author ORCID Information