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Title: Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT)

Abstract

Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic, barophilic, chemoorganotrophic thermophile is characterized by straight to curved Gram-negative rods. The strain described in this study was isolated from a core sample of deep sea sediments of the Peruvian high productivity upwelling system. This is the first completed genome sequence of a member of the genus Thermosediminibacter and the seventh genome sequence in the family Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285 protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [2];  [3];  [1];  [1];  [1];  [1];  [1];  [1];  [3];  [3];  [3];  [3];  [3];  [1];  [1];  [1];  [1];  [1];  [4] more »;  [4];  [5];  [5];  [5];  [5];  [2];  [6];  [6];  [6];  [1];  [1];  [7];  [4];  [1];  [1];  [6] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  6. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
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); German Research Foundation (DFG)
OSTI Identifier:
1630541
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-2; SI 1352/1-2
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 3; Journal Issue: 4; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; chemoorganotroph; anaerobe; thermophile; barophile; upwelling system; core sample; deep sea sediment; Thermoanaerobacterales; Firmicutes; GEBA

Citation Formats

Pitluck, Sam, Yasawong, Montri, Munk, Christine, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans-Peter. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT). United States: N. p., 2010. Web. doi:10.4056/sigs.1133078.
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Pitluck, Sam, Yasawong, Montri, Munk, Christine, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., & Klenk, Hans-Peter. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT). United States. https://doi.org/10.4056/sigs.1133078
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Pitluck, Sam, Yasawong, Montri, Munk, Christine, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans-Peter. Sun . "Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT)". United States. https://doi.org/10.4056/sigs.1133078. https://www.osti.gov/servlets/purl/1630541.
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@article{osti_1630541,
title = {Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT)},
author = {Pitluck, Sam and Yasawong, Montri and Munk, Christine and Nolan, Matt and Lapidus, Alla and Lucas, Susan and Glavina Del Rio, Tijana and Tice, Hope and Cheng, Jan-Fang and Bruce, David and Detter, Chris and Tapia, Roxanne and Han, Cliff and Goodwin, Lynne and Liolios, Konstantinos and Ivanova, Natalia and Mavromatis, Konstantinos and Mikhailova, Natalia and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Chang, Yun-Juan and Jeffries, Cynthia D. and Rohde, Manfred and Spring, Stefan and Sikorski, Johannes and Göker, Markus and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter},
abstractNote = {Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic, barophilic, chemoorganotrophic thermophile is characterized by straight to curved Gram-negative rods. The strain described in this study was isolated from a core sample of deep sea sediments of the Peruvian high productivity upwelling system. This is the first completed genome sequence of a member of the genus Thermosediminibacter and the seventh genome sequence in the family Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285 protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.1133078},
journal = {Standards in Genomic Sciences},
number = 4,
volume = 3,
place = {United States},
year = {Sun Oct 31 00:00:00 EDT 2010},
month = {Sun Oct 31 00:00:00 EDT 2010}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.4056/sigs.1133078
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Cited by: 9 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of T. oceani JW/IW-1228PT relative to the type strains of the other species within the family Thermoanaerobacteraceae. The trees were inferred from 1,316 aligned characters of the 16S rRNA gene sequence under the maximum likelihood criterion and rooted in accordance with the currentmore » taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 850 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD are shown in blue, published genomes in bold [CP001785,CP001145].« less
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