Whole-genome sequence of Sunxiuqinia dokdonensis DH1(T), isolated from deep sub-seafloor sediment in Dokdo Island.

Sunxiuqinia dokdonensis DH1(T) was isolated from deep sub-seafloor sediment at a depth of 900 m below the seafloor off Seo-do (the west part of Dokdo Island) in the East Sea of the Republic of Korea and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession LGIA00000000.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/assembly/GCF_001270965.1/.

Experimental design, materials and methods

Despite of extreme diversity in the deep sea environment, only a few kinds of microorganisms have been isolated and identified. Most of them are reported to belong to phylum of Bacteroidetes [1], [2], [3]. There are only four recognized species of the genus Sunxiuqinia, a member of the phylum Bacteroidetes; Sunxiuqinia elliptica, Sunxiuqinia rutila, Sunxiuqinia faeciviva and Sunxiuqinia dokdonensis. Among them, S. elliptica and S. rutile were isolated from shallow sea sediment in a sea cucumber farm and at Nagasuka Fishery Harbor, respectively. In contrast, S. dokdonensis and S. faeciviva were isolated from deep sub-seafloor sediment at a depth of 900 m below the seafloor off the west part of Dokdo Island and at a depth of 247.1 m below the seafloor off the Shimokita Peninsula, respectively [4], [5], [6], [7]. Based on difference of sampling depth, these two groups were clearly separated through the phylogenetic tree (Fig. 2). This is the first report of the whole genome sequence of the genus, Sunxiuqinia. This report would be helpful to extend our understanding about the genome and general characteristics of Sunxiuqinia for future studies of marine environment. DNA was extracted using bead-beating technique [8] and sequenced on HiSeq 2000 (Illumina). De novo genome assembly was performed using CLCbio CLC Genomics Workbench v7.5 and annotation was conducted on RAST [9]. SEED viewer was used for subsystem functional categorization of the predicted open reading frames (ORFs) and for visualization [10].

Fig. 2

Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the phylogentic position of strain DH1T and representative members of the genus Sunxiuqinia. Bootstrap values (expressed as percentages of 1,000 replication) are shown at branching points. Proloxobacter bellariivorans F2T was used as an outgroup. Bar, 0.02 substitution per nucleotide position.

Data description

Whole genome sequencing has generated and assembled into 225 contigs and the estimated genome size is 4,962,831 base pairs. The N50 of the genome is 43,403 bp and the G + C content of 45.4%. The genome was predicted to contain 4,550 coding sequence, 47 tRNAs and 3 rRNAs. These genes were annotated and classified into 385 subsystems (Fig. 1). Most of the annotated genes were involved in carbohydrate metabolism (378), amino acids and derivatives (336), protein metabolism (228), cofactors, vitamins, prosthetic groups and pigments formations (184), RNA metabolism (129) (Fig. 1), which is thought to be necessary to maintain the bacterial activity in the harsh environment like seafloor sediment. These genetic traits of marine isolate of Sunxiuqinia will provide a clue to the subsequent study of bacteria in the unique ocean ecosystem.

Fig. 1

Subsystems of Sunxiuqinia dokdonensis DH1T based on SEED database.

Nucleotide accession number

This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. LGIA00000000.

Conflict of interest

The authors clarified that this work and writing has no conflict of interest.

Specifications
Organism/cell line/tissue	Sunxiuqinia dokdonensis
Strain	DH1T
Sequencer or array type	HiSeq (Illumina)
Data format	Analyzed
Experimental factors	Microbial strain
Experimental features	Whole genome analysis and gene annotation of DH1T
Consent	N/A
Sample source location	Marine sediment in Dokdo Island