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The complete genome sequence of Rhodobacteraceae bacterium strain SH-1 isolated from a gut content of whiteleg shrimp Litopenaeus vannamei
Korean J. Microbiol. 2019;55(4):441-444
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Young-Sam Kim and Kyoung-Ho Kim*

Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
Correspondence to: *E-mail: kimkh@pknu.ac.kr;
Tel.: +82-51-629-5611; Fax: +82-51-629-5619
Received September 27, 2019; Revised December 2, 2019; Accepted December 2, 2019.
Abstract

Strain SH-1, a novel bacterium belonging to the family Rhodobacteraceae was isolated from a gut content of a whiteleg shrimp Litopenaeus vannamei collected from Tongyeong, South Korea. The complete genome sequence which is 3,892,138 bp with 66.1% G + C content was obtained using PacBio RS II platform. The genome annotation showed that the complete genome contains total 3,772 genes including 3,649 CDSs, 47 RNAs and 76 pseudogenes. Subsystems related to biosynthetic gene clusters for vitamins, amino acids and colicin V production protein were also predicted. The results may provide insights for understanding the symbiotic relationship between the strain and its host shrimp.

Keywords : Litopenaeus vannamei, Rhodobacteraceae, complete genome sequence, whiteleg shrimp
Body

One of the major aquatic bacterial groups in Alphaproteobacteria, the family Rhodobacteraceae is mainly found in various aquatic environments including fresh water and sea water. Currently, the family comprises more than 100 genera and 300 species and over 60% of them originated from marine environments (Simon et al., 2017). In marine environments, the family Rhodobacteraceae plays important roles in recycling of biochemical resources and symbiotic relationships with various marine eukaryote hosts (Elifantz et al., 2013; Simon et al., 2017). One of the marine invertebrates, a shrimp also has symbiotic relationship with its symbiotic microbiota including the family Rhodobacteraceae and studies about the bacterial diversity and interactions between a shrimp and its symbiotic microbiota showed that the microbiota produces various extracellular enzymes and metabolites which are beneficial for their hosts (Corbari et al., 2008; Tzuc et al., 2014; Cowart et al., 2017).

Strain SH-1 was isolated from the gut content of a whiteleg shrimp Litopenaeus vannamei collected from a shrimp farm (34° 51' 35.7" N 128° 26' 53" E, Tongyeong, South Korea) using serial dilution method after incubation on Marine Agar (MA, Difco) at 28°C for three days. The 16S rRNA sequence of the strain showed low sequence similarity compared to the close species Thalassococcushalodurans DSM 26915T [96.1%; Lee et al. (2007)], Phaeobactergallaeciensis DSM 26640T [96.09%; Martens et al. (2006)], and Pontibacamethylaminivorans DSM 21219T [96.03%; Kim et al. (2010)] which all belong to the family Rhodobacteraceae. Here, we present the genome features of the complete genome of a novel strain SH-1, which may provide insights into the symbiotic relationship in shrimps.

For whole genome sequencing, Genomic DNA Prep Kit (BIOFACT) was used to extract and purify the genomic DNA. PacBio RS II platform (Pacific Biosciences) yielded total 133,108 sequence reads, including 1,178,79,850 bases (N50, 12,787 bp; mean length, 8,855 bp) and de novo assembly of sequence reads was performed with Hierarchical Genome Assembly Process [HGAP, Version 3.0; Chin et al. (2013)]. The assembly generated a total of six contigs including one chromosome (3,892,138 bp with 66.1 mol% G + C content) and five plasmids (167,434 bp, 61.4 mol%; 78,245 bp, 60.8 mol%; 67,363 bp, 58.5 mol%; 41,166 bp, 61.8 mol%; 16,620 bp, 59 mol%). Rapid Annotations using Subsystems Technology [RAST; (http://rast.nmpdr.org/rast.cgi) Aziz et al. (2008)] and NCBI Prokaryotic Genome Annotation Pipeline [PGAP; Tatusova et al. (2016)] were used for the functional annotation and gene prediction, respectively. Total 3,772 genes including 3,649 CDSs, 47 RNAs and 76 pseudogenes were annotated by NCBI PGAP. Biosynthetic gene clusters related to vitamins and amino acids biosynthesis were also identified through RAST annotation.

CGView Comparison Tool (Grant et al., 2012) was used to assign genes to Clusters of Orthologous Groups (COGs) category and generate the circular genome map containing genome features (Fig. 1). One CRISPR locus was detected by CRISPRFinder [http://crispr.i2bc.paris-saclay.fr; Grissa et al. (2007)] and PHAge Search Tool Enhanced Release [PHASTER, http://phaster.ca/ ; Arndt et al. (2016)] detected three intact and one incomplete prophage sequences coding tail, head, terminase and phage related proteins of virus from chromosome sequence.

General features of Rhodobacteraceae sp. SH-1

FeatureValue
Genome size (bp)3,892,138
G + C content (%)66.1
Total genes3,772
Total CDS3,649
Genes assigned to COGs2,483
rRNAs (5S, 16S, 23S)1, 1, 1
tRNAs41
ncRNAs3
Pseudogenes76

Fig. 1.

Complete genome map of Rhodobacteraceae sp. SH-1. From the center to the outside: genome size label, GC skew (green and purple), G + C content (black), CDSs colored by COG categories on the reverse strand, CDSs including RNAs on the reverse strand, CDSs including RNAs on the forward strand, CDSs colored by COG categories on the forward strand.


The genome of strain SH-1, as a symbiotic bacterium of whiteleg shrimp, contained various biosynthetic gene clusters for vitamins, amino acids which might be beneficial for host and colicin V which inhibits other bacterial groups to be dominant in the gut environment. The result may provide a basis for understanding the symbiotic relationship in the host. Further experiments are in progress for identifying characteristics and comprehension of strain SH-1.

Nucleotide sequence accession number

The genome and plasmid sequences of Rhodobacteraceae bacterium strain SH-1 have been deposited at GenBank under the accession numbers of CP027665 and CP043619-CP043623, respectively. The strain has been deposited in the Korean Collection for Type Cultures (KCTC) with the preservation number KCTC 62276.

적 요

SH-1 균주는 Rhodobacteraceae 과에 속하는 신균으로서 대한민국의 통영에서 채취된 흰다리새우 Litopenaeusvannamei의 장내용물에서 분리되었다. PacBio RS II 분석법을 이용하여 얻어진 전장유전체의 길이는 3,892,138 bp이며 66.1%의 G + C 함유량을 가지고 있다. 이 유전체는 3,649개의 CDS와 47개의 RNA, 76개의 유사유전자를 포함하여 총 3,772개의 유전자를 가지고 있는 것으로 분석되었다. 콜리신 생산 단백질과 비타민 생합성 유전자 클러스와 관련된 하위체계(subsystem)가 존재하는 것이 확인되었다. 본 결과는 이 균주와 숙주인 새우의 공생관계를 이해하는데 도움을 줄 것이다.

Acknowledgements

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2016R1D1A3B 04935909).

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December 2019, 55 (4)