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Draft genome sequence of a marine Flavobacteria Flagellimonas eckloniae DOKDO 007T
Korean J. Microbiol 2018;54(4):460-462
Published online December 31, 2018
© 2018 The Microbiological Society of Korea.

Yong Min Kwon1, Patra Ajit Kumar1, Sang-Jin Kim1,2, and Kae Kyoung Kwon2,*

1National Marine Biodiversity Institute of Korea, Seocheon 33662, Republic of Korea,
2Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Pusan 49111, Republic of Korea
Correspondence to: E-mail: kkkwon@kiost.ac.kr; Tel.: +82-51-664-3371; Fax: +82-51-955-3981
Received October 22, 2018; Revised November 8, 2018; Accepted November 8, 2018.
Abstract

Flagellimonas eckloniae DOKDO 007T, isolated from the rhizosphere of the marine algae Ecklonia kurome collected from Dokdo Island, South Korea, is a marine Flavobacteria belonging to the family Flavobacteriaceae. The genome consists of 4,132,279 bp, 3,527 coding sequences with 37.85% G + C contents and two contigs in one scaffold chromosome. This strain contains a gene encoding proteorhodopsin, as well as other retinal biosynthesis genes, allowing it to utilize sunlight as an energy source. The strain contained only few segment of flagellar constructing gene cluster and this is not consistent with genus name Flagellimonas, therefore, revision of the genus name is required.

Keywords : Flagellimonas eckloniae, genome sequence, marine Flavobacteria, proteorhodopsin
Body
he genus Flagellimonas is a part of the family Flavobacteriaceae, one of the major phylogenetic lineages within the phylum Bacteroidetes (Garrity and Holt, 2001). Flavobacteria play a pivotal role in the photometabolic system in marine environments (Fuhrman et al., 2008). The genus Flagellimonas was proposed by Bae et al. (2007), with the description of Flagellimonas eckloniae as the type species and recently emended by Choi et al. (2018) with a new species F. aquimarina and combination with the genus Spongiibacterium Yoon and Oh 2012. The strain DOKDO 007T is an orange-pigmented, aerobic, Gram-negative, rod-shaped marine Flavobacteria, which was isolated from the rhizosphere of the marine macroalgae Ecklonia kurome and collected along the seashore of Dokdo Island, South Korea (Bae et al., 2007). Therefore, addition of the information on the draft genome to the data on the genus Flagellimonas provides an opportunity for comparative genome analyses and serves as a resource for understanding the evolution and molecular mechanisms for adaptation of Flagellimonas species in the rhizosphere of the marine macroalgae.

The DOKDO 007T genome sequencing was undertaken using PacBio RS II single-molecule real-time (SMRT) sequencing technology. A 10-kb insert library was constructed and sequenced, yielding > 161.8 × average genome coverage. De novo assembly of the 136,261 reads (668,421,644 bp in total) was conducted using the hierarchical genome-assembly process pipeline of SMRT Analysis v2.2.0. Open reading frames were predicted using the National Centre for Biotechnology Information Prokaryotic Genomes Annotation Pipeline and the genome was submitted to the Integrated Microbial Genomes server of the Joint Genome Institute for Cluster of Orthologous Groups (COG) analysis.

The draft genome of Flagellimonas eckloniae DOKDO 007T consists of 4,132,279 bp, with 37.85% GC content and two contigs in one scaffold chromosome without plasmids (Table 1). The coding regions cover 90.38% of the genome (3,734,922 bp) and encode 3,527 proteins (Table 1); of these, 1,903 (53.28%) were assigned to COGs. The most abundant COG category was ‘General function prediction only’ (207 proteins), followed by ‘Translation, ribosomal structure, and biogenesis’ (177 proteins) and ‘Amino acid transport and metabolism’ (170 proteins). Additionally, the genome encodes 142 pseudo-genes, 6 rRNAs, and 38 tRNAs with a single rRNA operon (Table 1).

General features of Flagellimonas eckloniae DOKDO 007T

 FeaturesChromosome
Genome size (bp)4,132,279
DNA coding region (bp)3,734,922
GC content (%)37.85
Contig2
Plasmid0
Protein coding genes3,527
rRNA (5S, 16S, 23S)6 (2, 2, 2)
tRNA38
ncRNA1
Genes with functional prediction2,703
Genes assigned to COGs1,903
Genes with Pfam domains2,721
Genes with signal peptides349
Genes with transmembrane helices789
Pseudo genes142

The genome analysis of strain DOKDO 007T revealed the presence of a green light-absorbing proteorhodopsin (PR) of 242 amino acid residues. Several important residues necessary for energy generation are conserved among rhodopsins, including Asp97, Glu108, and Lys216 (Béjà et al., 2000; Man et al., 2003; Fuhrman et al., 2008). The PR sequence of DOKDO 007T is closest to that of the Muricauda pacifica DSM 25027T with 90% sequence identity according to BLAST analysis. Additionally, the blh gene encoding a 15,15’-β-carotene dioxygenase was located adjacent to the PR gene, similar to the genes in other PR-containing Bacteriodetes genomes and putative retinal-producing biosynthetic pathway genes (Béjà et al., 2000; Teramoto et al., 2003; Gómez-Consarnau et al., 2007; Kimura et al., 2011). One of the remarkable feature is that only few no. of flagellar construction related genes were detected from the genome sequence and this was consistent with the result of Choi et al. (2018). Therefore, emendation of the genus name “Flagellimonas” is required.

Strain and nucleotide sequence accession numbers

The draft genome sequence of Flagellimonas eckloniae DOKDO 007T has been deposited at DDBJ/EMBL/GenBank under accession number LCTZ00000000. The strain is available from Marine & Extreme Bioresource Collection (http://www.megrc.re.kr/mebic/mebic_l1/eng/html/intro_mebic.asp), under the code MEBiC01917T.

적 요

Flavobacteriaceae에 속하는 해양 FlavobacteriaFlagellimonas eckloniae DOKDO 007T은 독도에서 서식하는 조류(Ecklonia kurome)에서 분리되었다. DOKDO 007T균주의 유전체는 4,132,279 bp 크기로 3,527개의 코딩 서열과 37.85%의 GC 함량을 가지며, 하나의 스케폴드에서 두 개의 콘티그로 구성되어 있다. 이 균주는 태양광을 에너지원으로써 이용할 수 있는 여러 레티날 생합성 유전자들과 마찬가지로 프로테오로돕신을 인코딩하는 유전자를 함유하고 있다. 속명과는 달리 편모 형성에 관여하는 유전자가 충분하지 못한 것을 감안하여 속명의 개정이 필요하다.

Acknowledgements

This work was supported by the MABIK in-house program (2018M00600) and the KIOST in-house program (PE99622). We thank Marine & Extreme Bioresource Collection (MEBiC) at KIOST for providing marine Flavobacteria isolate.

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