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Title: Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)

Abstract

Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus Dethiosulfovibrio of the family Synergistaceae in the recently created phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids. It was isolated from an offshore oil well where it was been reported to be involved in pitting corrosion of mild steel. Initially, this bacterium was described as a distant relative of the genus Thermoanaerobacter, but was not assigned to a genus, it was subsequently placed into the novel phylum Synergistetes. A large number of repeats in the genome sequence prevented an economically justifiable closure of the last gaps. This is only the third published genome from a member of the phylum Synergistetes. The 2,576,359 bp long genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [3];  [4];  [4];  [5];  [5];  [5] more »;  [5];  [6];  [7];  [7];  [1];  [1];  [8];  [4];  [1];  [1];  [7];  [1] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Inst. of Microbial Technology, Chandigarh (India); German Collection of Microorganisms and Cell Culture, 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); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
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); German Research Foundation (DFG)
OSTI Identifier:
1630555
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-2
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; anaerobic; motile; vibrio-shaped; thiosulfate-reducing; H2S producing; peptide utilization; Synergistaceae; Synergistetes; GEBA

Citation Formats

LaButti, Kurt, Mayilraj, Shanmugam, Clum, Alicia, Lucas, Susan, Glavina Del Rio, Tijana, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Lapidus, Alla. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T). United States: N. p., 2010. Web. doi:10.4056/sigs.1092865.
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LaButti, Kurt, Mayilraj, Shanmugam, Clum, Alicia, Lucas, Susan, Glavina Del Rio, Tijana, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, & Lapidus, Alla. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T). United States. https://doi.org/10.4056/sigs.1092865
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LaButti, Kurt, Mayilraj, Shanmugam, Clum, Alicia, Lucas, Susan, Glavina Del Rio, Tijana, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Lapidus, Alla. Mon . "Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)". United States. https://doi.org/10.4056/sigs.1092865. https://www.osti.gov/servlets/purl/1630555.
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@article{osti_1630555,
title = {Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)},
author = {LaButti, Kurt and Mayilraj, Shanmugam and Clum, Alicia and Lucas, Susan and Glavina Del Rio, Tijana and Nolan, Matt and Tice, Hope and Cheng, Jan-Fang and Pitluck, Sam and Liolios, Konstantinos and Ivanova, Natalia and Mavromatis, Konstantinos and Mikhailova, Natalia and Pati, Amrita and Goodwin, Lynne 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 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 and Lapidus, Alla},
abstractNote = {Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus Dethiosulfovibrio of the family Synergistaceae in the recently created phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids. It was isolated from an offshore oil well where it was been reported to be involved in pitting corrosion of mild steel. Initially, this bacterium was described as a distant relative of the genus Thermoanaerobacter, but was not assigned to a genus, it was subsequently placed into the novel phylum Synergistetes. A large number of repeats in the genome sequence prevented an economically justifiable closure of the last gaps. This is only the third published genome from a member of the phylum Synergistetes. The 2,576,359 bp long genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.1092865},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 3,
place = {United States},
year = {Mon Aug 30 00:00:00 EDT 2010},
month = {Mon Aug 30 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.1092865
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Cited by: 7 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of D. peptidovorans SEBR 4207T relative to the other type strains within the phylum Synergistetes. The tree was inferred from 1,328 aligned characters of the 16S rRNA gene sequence under the maximum likelihood criterion and rooted in accordance with the current taxonomy. Themore » branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if greater than 60%. Lineages with type strain genome sequencing projects registered in GOLD are shown in blue, published genomes in bold.« less
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