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Title: High-quality draft genome sequence of Gracilimonas tropica CL-CB462T (DSM 19535T), isolated from a Synechococcus culture

Abstract

Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535T, was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. Finally, the strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535T did not form spore.

Authors:
 [1];  [1];  [1];  [2];  [3];  [3];  [3];  [4];  [3];  [5];  [6];  [7];  [7];  [3];  [8];  [9];  [1]
  1. Seoul National Univ. (Korea, Republic of)
  2. St. Petersburg State Univ., St. Petersburg (Russia); St. Petersburg Academic Univ., St. Petersburg, (Russia)
  3. DOE Joint Genome Institute, Walnut Creek, CA (United States). Genome Biology Program
  4. St. Petersburg Academic Univ., St. Petersburg, (Russia)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. HZI - Helmholtz Centre for Infection Research, Braunschweig (Germany). Central Facility for Microscopy
  7. Leibniz Institute DSMZ, Braunschweig (Germany)
  8. Leibniz Institute DSMZ, Braunschweig (Germany); Newcastle Univ., Newcastle upon Tyne (United Kingdom)
  9. DOE Joint Genome Institute, Walnut Creek, CA (United States). Genome Biology Program; King Abdulaziz Univ., Jeddah (Saudi Arabia)
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:
1256942
Alternate Identifier(s):
OSTI ID: 1378642
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genome; Gracilimonas tropica; Marine; Sphingobacteriia; GEBA

Citation Formats

Choi, Dong Han, Ahn, Chisang, Jang, Gwang Il, Lapidus, Alla, Han, James, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Rohde, Manfred, Tindall, Brian, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Cho, Byung Cheol. High-quality draft genome sequence of Gracilimonas tropica CL-CB462T (DSM 19535T), isolated from a Synechococcus culture. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0088-8.
Choi, Dong Han, Ahn, Chisang, Jang, Gwang Il, Lapidus, Alla, Han, James, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Rohde, Manfred, Tindall, Brian, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., & Cho, Byung Cheol. High-quality draft genome sequence of Gracilimonas tropica CL-CB462T (DSM 19535T), isolated from a Synechococcus culture. United States. doi:10.1186/s40793-015-0088-8.
Choi, Dong Han, Ahn, Chisang, Jang, Gwang Il, Lapidus, Alla, Han, James, Reddy, T. B. K., Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Rohde, Manfred, Tindall, Brian, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C., and Cho, Byung Cheol. Wed . "High-quality draft genome sequence of Gracilimonas tropica CL-CB462T (DSM 19535T), isolated from a Synechococcus culture". United States. doi:10.1186/s40793-015-0088-8. https://www.osti.gov/servlets/purl/1256942.
@article{osti_1256942,
title = {High-quality draft genome sequence of Gracilimonas tropica CL-CB462T (DSM 19535T), isolated from a Synechococcus culture},
author = {Choi, Dong Han and Ahn, Chisang and Jang, Gwang Il and Lapidus, Alla and Han, James and Reddy, T. B. K. and Huntemann, Marcel and Pati, Amrita and Ivanova, Natalia and Markowitz, Victor and Rohde, Manfred and Tindall, Brian and Göker, Markus and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C. and Cho, Byung Cheol},
abstractNote = {Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535T, was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. Finally, the strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535T did not form spore.},
doi = {10.1186/s40793-015-0088-8},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {2015},
month = {11}
}

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