Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5

Kiyoung Yoon; Ju Yeon Song; Min-Jung Kwak; Soon-Kyeong Kwon; Jihyun F. Kim

doi:10.1007/s12275-017-6427-2

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Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5: Kiyoung Yoon ¹, Ju Yeon Song ¹, Min-Jung Kwak ¹, Soon-Kyeong Kwon ¹, Jihyun F. Kim ^1,2; Journal of Microbiology 2017;55(7):561-567.
DOI: https://doi.org/10.1007/s12275-017-6427-2
Published online: April 22, 2017

¹Department of Systems Biology, Division of Life Sciences, ²Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Republic of Korea¹Department of Systems Biology, Division of Life Sciences, ²Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Republic of Korea

Corresponding author: Jihyun F. Kim , Tel: +82-2-2123-5561,

Received: 29 August 2016 • Revised: 6 March 2017 • Accepted: 22 March 2017

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Abstract

Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes. Comparison of average nucleotide identities among six available Polaribacteria genomes including DSW-5 suggested that the DSW-5 genome is most similar to that of Polaribacter sp. MED152, which is a proteorhodopsin-containing marine bacterium. A phylogenomic analysis of the six Polaribacter strains and 245 Flavobacteriaceae bacteria confirmed a close relationship of the genus Polaribacter with Tenacibaculum and Kordia. DSW-5’s genome has a gene encoding proteorhodopsin and genes encoding 85 enzymes belonging to carbohydrate-active enzyme families and involved in polysaccharide degradation, which may play important roles in energy metabolism of the bacterium in the marine ecosystem. With genes for 238 CAZymes and 203 peptidases, DSW-5 has a relatively high number of degrading enzymes for its genome size suggesting its characteristics as a free-living marine heterotroph.

Keywords: Bacteriodetes;microbial rhodopsin;Dokdonia;Nonlabens

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Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5

J. Microbiol. 2017;55(7):561-567. Published online April 22, 2017

DOI: https://doi.org/10.1007/s12275-017-6427-2

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