A novel Rhodobacteraceae bacterium, strain SC52 was isolated

from the gut content of a sea cucumber Apostichopus japonicus

collected from the coastal sea near Namhae, Republic of Korea.

The strain was distantly related to known species within the

family Rhodobacteraceae (below 95.9% in 16S rRNA gene

comparison). One chromosome (2.6 Mbp), seven circular

plasmids (15 kb~391 kb), and one linear plasmid (7 kb)

sequences (a total of 3,893,634 bp) were obtained by using

PacBio RS II platform. A total of 3,853 genes, 3,794 CDSs, 49

tRNAs, and 9 rRNAs were annotated in the contigs. Genome

annotation identified genes related to biosynthesis of possible

nutrient sources such as various vitamins and amino acids,

which will contribute to investigate the genetic diversity of the

Rhodobacteraceae group that was frequently detected in the

sea cucumbers.

Keywords: Apostichopus japonicus, Rhodobacteraceae, complete

genome sequence, sea cucumber

The family Rhodobacteraceae is one of the major bacterial

groups within the phylum Proteobacteria and harbors many

aquatic bacteria inhabiting freshwater and marine environments

(Elifantz et al., 2013). The members of Rhodobacteraceae

have diverse physiologic and metabolic characteristics and are

often found in marine animals as symbiotic bacteria (Pujalte et

al., 2014). Previous studies also reported that members of

Rhodobacteraceae were frequently detected as a core group in

the intestine of A. japonicus based on the culture-independent

analysis (Sha et al., 2016; Wang et al., 2018; Zhang et al.,

2019). Isolation and whole genome sequencing analysis of a

novel strain will help us to understand the roles of the

Rhodobacteraceae group in sea cucumbers.

Strain SC52 was isolated by standard dilution plating

method from the gut content of a sea cucumber Apostichopus

japonicus collected from the coastal sea near Namhae, South

Korea, after incubation at 25°C for 3 days on marine agar (MA,

Difco). The phylogenetic analysis showed that strain SC52

formed a phylogenetic lineage with Meridianimarinicoccus

roseus TG-679T (with 95.9% of 16S rRNA sequence similarity),

Ruegeria lacuscaerulensis ITI-1157T (95.3%) and Epibacterium

mobile DSM 23403T (95.2%). Genomic DNA of strain SC52

was extracted using a genomic DNA extraction kit (BIOFACT)

and sequenced by PacBio RSII platform (Pacific Biosciences).

Korean Journal of Microbiology (2020) Vol. 56, No. 2, pp. 186-189 pISSN 0440-2413DOI https://doi.org/10.7845/kjm.2020.0044 eISSN 2383-9902Copyright ⓒ 2020, The Microbiological Society of Korea

Whole genome sequence of Rhodobacteraceae strain SC52 from gut

content of sea cucumber Apostichopus japonicus

Sang-Eon Kim1†, Young-Sam Kim1†, and Kyoung-Ho Kim1,2*

1Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea2School of Marine and Fisheries Life Science, Pukyong National University, Busan 48513, Republic of Korea

해삼 Apostichopus japonicus의 장 내에서 분리된

Rhodobacteraceae sp. SC52의 전장유전체

김상언1† ･ 김영삼1† ･ 김경호1,2*1부경대학교 미생물학과, 2부경대학교 해양수산생명과학부

(Received May 12, 2020; Revised June 8, 2020; Accepted June 15, 2020)

†The authors contributed equally to this work.

*For correspondence. E-mail: kimkh@pknu.ac.kr;

Tel.: +82-51-629-5611; Fax: +82-51-629-5619

Complete genome sequence of Rhodobacteraceae strain SC52 ∙ 187

Korean Journal of Microbiology, Vol. 56, No. 2

Through the single-molecule real-time sequencing of PacBio, a

total of 135,690 subreads (total subread base, 1,345,248,063;

N50, 13,830; mean subread length, 9,914) were yielded. The

subreads were then de novo assembled by Hierarchical

Genome Assembly Process [HGAP, Version 3.0; Chin et al.

(2013)] and a total of nine contigs including one chromosome

(2,627,566 bp with 58.74 mol% G + C content) and eight

plasmids (391,128 bp with 57.77 mol%; 352,381 bp with 56.64

mol%; 273,781 bp with 57.51 mol%; 101,226 bp with 60.05

mol%; 65,203 bp with 58.88 mol%; 60,660 bp with 60.56

Table 1. Genomic features of contigs of strain SC52

Contig Genome size (bp) G + C content (%) Circular Gene CDS tRNA rRNA COG

SC52 2,627,566 58.74 Yes 2,671 2,620 44 6 1,903

pSC52_1 391,128 57.77 Yes 347 345 2 0 226

pSC52_2 352,381 56.64 Yes 322 316 3 3 223

pSC52_3 273,781 57.51 Yes 246 246 0 0 165

pSC52_4 101,226 60.05 Yes 119 119 0 0 76

pSC52_5 65,203 58.88 Yes 75 75 0 0 59

pSC52_6 60,660 60.56 Yes 45 45 0 0 22

pSC52_7 14,858 56.03 Yes 18 18 0 0 7

pSC52_8 6,831 58.62 No 10 10 0 0 5

Fig. 1. Genome maps of nine contigs of strain SC52. From inside: GC skew (green and purple), G + C content (black), CDSs with multi-colored of COG

categories on the reverse direction, CDSs in reverse direction including RNA, CDSs in forward direction including RNA, CDSs with multi-colored of COG

categories on the forward direction. The scale of each map does not reflect actual size.

188 ∙ Kim et al.

미생물학회지 제56권 제2호

mol%; 14,858 bp with 56.03 mol%; 6.831 bp with 58.62 mol%)

were obtained.

Contigs were subjected to NCBI Prokaryotic Genome

Annotation Pipeline (PGAP) (Tatusova et al., 2016) and a total

of 3,853 genes, 3,794 CDSs, 49 tRNAs, and 9 rRNAs were

annotated (Table 1). CGView Comparison Tool [CCT; Grant

et al. (2012)] was used to construct genome maps presenting

genomic features and assigned Clusters of Orthologous Groups

(COGs) categories (Fig. 1). PHAge Search Tool Enhanced

Release [PHASTER; http://phaster.ca/; Arndt et al. (2016)]

detected one questionable and one incomplete prophage

sequences coding attachment proteins and viral head proteins

from the chromosome. Rapid Annotations using Subsystems

Technology [RAST; http://rast.nmpdr.org/rast.cgi; Aziz et al.

(2008)] identified gene clusters related to the biosynthesis of

various vitamins including thiamin (thiamin phosphate synthase

YjbQ; G5B39_09705), cobalamin (cobalamin biosynthesis

protein CbiD, CobD/CbiB, CobN, CobT, and cobalamin

synthase; G5B39_05710, 01605, 04045, 10005, 07215, and

08650), pyridoxine (pyridoxine 5'-phosphate synthase PdxJ;

G5B39_01030), and folate (dihydrofolate reductase; G5B39_

08470) and amino acids including glutamine (glutamine

synthetase GlnA and glutamate synthase domain 2 GltB;

G5B39_02735 and G5B39_06950), glutamate [N-acetylglutamate

synthase (N-acetylornithine aminotransferase) ArgJ; G5B39_

01810), histidine (phosphohistidine phosphatase SixA; G5B39_

04915), arginine [arginine decarboxylase (spermidine biosyn-

thesis) SpeA; G5B39_07850), threonine (threonine synthase

and threonine dehydratase EutB and IlvA; G5B39_00820,

G5B39_06385, and G5B39_01670), tryptophan (tryptophan

synthase beta chain TrpB and tryptophanyl-tRNA synthetase

TrpS; G5B39_00235 and G5B39_05265), glycine (glycine

cleavage system protein GcvH, GcvP, and GcvT; G5B39_

07050, G5B39_07045, and G5B39_07055), alanine (alanine

dehydrogenase Ald, and alanine racemase Alr; G5B39_01890

and G5B39_05670), and serine (phosphoserine phosphatase

SerB, and serine acetyltransferase CysE; G5B39_03190 and

G5B39_06610).

It was reported that amino acids such as threonine, leucine,

histidine and arginine efficiently increased the growth rate of

sea cucumber (Huiling et al., 2005). Sea cucumbers ingest

bacteria and bacterial cell components could be important food

sources for A. japonicus (Gao et al., 2014; Pagan-Jimenez et

al., 2019). The genomic properties of the strain SC52 might

give a clue for its role in the nutrition of sea cucumbers, which

should be investigated through further researches.

Nucleotide sequence accession number

The strain was deposited at the Korean Collection for Type

Cultures with accession number KCTC 72133 and the

complete genome sequences including chromosome and

plasmids of strain SC52 were deposited in GenBank under

accession numbers CP049028-CP049036.

적 요

신종 균주 SC52는 한국의 남해 연안에서 채집된 해삼

Apostichopus japonicus의 장에서 분리되었다. 이 균주는 기존

에 알려진 Rhodobacteraceae 과에 속하는 균주들과 유사도가

낮은 것(16S rRNA 유전자 유사도 95.9% 이하)으로 확인되었

다. 유전체 서열을 PacBio RS II를 이용하여 분석한 결과, 하나

의 염색체(2.6 Mbp)와 일곱 개의 원형 플라스미드(15 kb~391

kb) 그리고 한 개의 선형(7 kb) 플라스미드 서열이 확인되었으

며, 총 3,853개의 유전자, 3,794개의 CDS, 49개의 tRNA 그리

고 9개의 rRNA 서열이 포함된 것으로 나타났다. 유전체 분석

결과 영양분으로 사용될 수 있는 다양한 비타민과 아미노산의

생합성 관련 유전자들이 확인되었으며 이는 해삼에서 자주 발

견되는 Rhodobacteraceae 집단의 유전적 다양성을 연구하는

데 기여할 것이다.

Acknowledgments

This research was supported by Basic Science Research

Program through the National Research Foundation of Korea

(NRF) funded by the Ministry of Education (2016R1D1A3

B04935909).

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