Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), 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-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.
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618977
- Alternate Identifier(s):
- OSTI ID: 1419442
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 12 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- 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., Göker, 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 Kingdom: 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., Göker, 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 Kingdom. https://doi.org/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., Göker, 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 Kingdom. https://doi.org/10.1186/s40793-017-0275-x.
@article{osti_1618977,
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 Göker, 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 Kingdom},
year = {Mon Oct 30 00:00:00 EDT 2017},
month = {Mon Oct 30 00:00:00 EDT 2017}
}
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https://doi.org/10.1186/s40793-017-0275-x
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Figures / Tables:
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 »
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Figures / Tables found in this record:
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