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Title: Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring

Abstract

Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [1];  [1];  [2];  [3];  [2];  [2];  [2];  [2];  [2];  [3];  [3];  [3];  [2];  [2];  [2];  [2];  [2];  [2];  [2] more »;  [4];  [4];  [5];  [5];  [5];  [5];  [6];  [3];  [2];  [2];  [7];  [4];  [8];  [9];  [1];  [10] « less
  1. Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  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. HZI - Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California Davis Genome Center, Davis, CA (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); The Univ. of Queensland, Brisbane (Australia)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  10. St. Petersburg State Univ., St. Petersburg (Russia); St. Petersburg Academic Univ., St. Petersburg (Russia)
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:
1378618
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal Issue: 3; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; anaerobic; motile; thermophilic; chemoorganotrophic; solfataric spring; outer sheath-like structure; Thermotogaceae; GEBA

Citation Formats

Goker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan -Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans -Peter, and Lapidus, Alla. Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. United States: N. p., 2014. Web. doi:10.4056/sigs.3016383.
Goker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan -Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans -Peter, & Lapidus, Alla. Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. United States. https://doi.org/10.4056/sigs.3016383
Goker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan -Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans -Peter, and Lapidus, Alla. Sun . "Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring". United States. https://doi.org/10.4056/sigs.3016383. https://www.osti.gov/servlets/purl/1378618.
@article{osti_1378618,
title = {Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring},
author = {Goker, Markus and Spring, Stefan and Scheuner, Carmen and Anderson, Iain and Zeytun, Ahmet and Nolan, Matt and Lucas, Susan and Tice, Hope and Del Rio, Tijana Glavina and Cheng, Jan -Fang and Han, Cliff and Tapia, Roxanne and Goodwin, Lynne A. and Pitluck, Sam and Liolios, Konstantinos and Mavromatis, Konstantinos and Pagani, Ioanna and Ivanova, Natalia 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 Detter, John C. and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans -Peter and Lapidus, Alla},
abstractNote = {Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.3016383},
journal = {Standards in Genomic Sciences},
number = 3,
volume = 9,
place = {United States},
year = {Sun Jun 15 00:00:00 EDT 2014},
month = {Sun Jun 15 00:00:00 EDT 2014}
}

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