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

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Bacteria in the genus Polaribacter, belonging to the family 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.

Original languageEnglish
Pages (from-to)561-567
Number of pages7
JournalJournal of Microbiology
Volume55
Issue number7
DOIs
Publication statusPublished - 2017 Jul 1

Fingerprint

Flavobacterium
Genome
Flavobacteriaceae
Bacteria
Tenacibaculum
Genes
Enzymes
Genome Size
Firearms
Korea
Gram-Negative Bacteria
Oceans and Seas
Energy Metabolism
Polysaccharides
Ecosystem
Peptide Hydrolases
Nucleotides
Carbohydrates
proteorhodopsin

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Applied Microbiology and Biotechnology

Cite this

Yoon, Kiyoung ; Song, Ju Yeon ; Kwak, Min Jung ; Kwon, Soon Kyeong ; Kim, Jihyun F. / Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5. In: Journal of Microbiology. 2017 ; Vol. 55, No. 7. pp. 561-567.
@article{f71fb437356e4273becffb8edece394d,
title = "Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5",
abstract = "Bacteria in the genus Polaribacter, belonging to the family 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.",
author = "Kiyoung Yoon and Song, {Ju Yeon} and Kwak, {Min Jung} and Kwon, {Soon Kyeong} and Kim, {Jihyun F.}",
year = "2017",
month = "7",
day = "1",
doi = "10.1007/s12275-017-6427-2",
language = "English",
volume = "55",
pages = "561--567",
journal = "Journal of Microbiology",
issn = "1225-8873",
publisher = "Microbiological Society of Korea",
number = "7",

}

Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5. / Yoon, Kiyoung; Song, Ju Yeon; Kwak, Min Jung; Kwon, Soon Kyeong; Kim, Jihyun F.

In: Journal of Microbiology, Vol. 55, No. 7, 01.07.2017, p. 561-567.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5

AU - Yoon, Kiyoung

AU - Song, Ju Yeon

AU - Kwak, Min Jung

AU - Kwon, Soon Kyeong

AU - Kim, Jihyun F.

PY - 2017/7/1

Y1 - 2017/7/1

N2 - Bacteria in the genus Polaribacter, belonging to the family 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.

AB - Bacteria in the genus Polaribacter, belonging to the family 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.

UR - http://www.scopus.com/inward/record.url?scp=85018809077&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85018809077&partnerID=8YFLogxK

U2 - 10.1007/s12275-017-6427-2

DO - 10.1007/s12275-017-6427-2

M3 - Article

C2 - 28432541

AN - SCOPUS:85018809077

VL - 55

SP - 561

EP - 567

JO - Journal of Microbiology

JF - Journal of Microbiology

SN - 1225-8873

IS - 7

ER -