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Title: Draft genome sequence of Marinobacterium rhizophilum CL-YJ9 T (DSM 18822 T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica

Abstract

The genus Marinobacterium belongs to the family Alteromonadaceae within the class Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium contains 16 species. Marinobacterium rhizophilum CL-YJ9 T was isolated from sediment associated with the roots of a plant growing in a tidal flat of Youngjong Island, Korea. The genome of the strain CL-YJ9 T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report the main features of the draft genome of the strain. The 5,364,574 bp long draft genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based on the genomic analyses, the strain seems to adapt to osmotic changes by intracellular production as well as extracellular uptake of compatible solutes, such as ectoine and betaine. In addition, the strain has a number of genes to defense against oxygen stresses such as reactive oxygen species and hypoxia.

Authors:
 [1];  [2];  [3];  [4];  [4];  [4];  [4];  [5];  [4];  [6];  [7];  [7];  [4];  [8];  [4];  [2]
  1. Korea Institute of Ocean Science and Technology, Ansan (Republic of Korea)
  2. Seoul National Univ., Seoul (Republic of Korea)
  3. St. Petersburg State Univ., St. Petersburg (Russia); St. Petersburg Academic Univ., St. Petersburg (Russia)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. St. Petersburg Academic Univ., St. Petersburg (Russia)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  7. Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  8. Newcastle Univ., Newcastle upon Tyne (United Kingdom)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1419442
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
[ Journal Volume: 12; Journal Issue: 1]; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genome; Marinobacterium rhizophilum; Suaeda Japonica; Rhizosphere; GEBA

Citation Formats

Choi, Dong Han, Jang, Gwang II, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Mukherjee, Supratim, Huntemann, Marcel, Varghese, Neha, Ivanova, Natalia, Pillay, Manoj, Tindall, Brian J., Goker, Markus, Woyke, Tanja, Klenk, Hans -Peter, Kyrpides, Nikos C., and Cho, Byung Cheol. Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0275-x.
Choi, Dong Han, Jang, Gwang II, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Mukherjee, Supratim, Huntemann, Marcel, Varghese, Neha, Ivanova, Natalia, Pillay, Manoj, Tindall, Brian J., Goker, Markus, Woyke, Tanja, Klenk, Hans -Peter, Kyrpides, Nikos C., & Cho, Byung Cheol. Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica. United States. doi:10.1186/s40793-017-0275-x.
Choi, Dong Han, Jang, Gwang II, Lapidus, Alla, Copeland, Alex, Reddy, T. B. K., Mukherjee, Supratim, Huntemann, Marcel, Varghese, Neha, Ivanova, Natalia, Pillay, Manoj, Tindall, Brian J., Goker, Markus, Woyke, Tanja, Klenk, Hans -Peter, Kyrpides, Nikos C., and Cho, Byung Cheol. Mon . "Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica". United States. doi:10.1186/s40793-017-0275-x. https://www.osti.gov/servlets/purl/1419442.
@article{osti_1419442,
title = {Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica},
author = {Choi, Dong Han and Jang, Gwang II and Lapidus, Alla and Copeland, Alex and Reddy, T. B. K. and Mukherjee, Supratim and Huntemann, Marcel and Varghese, Neha and Ivanova, Natalia and Pillay, Manoj and Tindall, Brian J. and Goker, Markus and Woyke, Tanja and Klenk, Hans -Peter and Kyrpides, Nikos C. and Cho, Byung Cheol},
abstractNote = {The genus Marinobacterium belongs to the family Alteromonadaceae within the class Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium contains 16 species. Marinobacterium rhizophilum CL-YJ9T was isolated from sediment associated with the roots of a plant growing in a tidal flat of Youngjong Island, Korea. The genome of the strain CL-YJ9T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report the main features of the draft genome of the strain. The 5,364,574 bp long draft genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based on the genomic analyses, the strain seems to adapt to osmotic changes by intracellular production as well as extracellular uptake of compatible solutes, such as ectoine and betaine. In addition, the strain has a number of genes to defense against oxygen stresses such as reactive oxygen species and hypoxia.},
doi = {10.1186/s40793-017-0275-x},
journal = {Standards in Genomic Sciences},
number = [1],
volume = [12],
place = {United States},
year = {2017},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Fig. 1 Fig. 1: Neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, showing the relationships between strain CL-YJ9T, members of the genus Marinobacterium and other related genera. Bootstrap percentages >60% (based on 1000 resamplings) are shown below or above the corresponding branches. Solid circles indicate that the corresponding nodes are alsomore » recovered in the maximum-likelihood and maximum-parsimony trees. Terasakiella pusillum IFO 13613T (AB006768) was used as an outgroup. Bar, 0.02 nucleotide substitutions per site« less

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