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

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

doi:10.4056/sigs.1092865

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

Journal Article · Mon Aug 30 00:00:00 EDT 2010 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1092865· OSTI ID:1630555

LaButti, Kurt ^[1]; Mayilraj, Shanmugam ^[2]; Clum, Alicia ^[1]; Lucas, Susan ^[1]; Glavina Del Rio, Tijana ^[1]; Nolan, Matt ^[1]; Tice, Hope ^[1]; Cheng, Jan-Fang ^[1]; Pitluck, Sam ^[1]; Liolios, Konstantinos ^[1]; Ivanova, Natalia ^[1]; Mavromatis, Konstantinos ^[1]; Mikhailova, Natalia ^[1]; Pati, Amrita ^[1]; Goodwin, Lynne ^[3]; Chen, Amy ^[4]; Palaniappan, Krishna ^[4]; Land, Miriam ^[5]; Hauser, Loren ^[5]; Chang, Yun-Juan ^[5] more »

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Inst. of Microbial Technology, Chandigarh (India); German Collection of Microorganisms and Cell Culture, Braunschweig (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Helmholtz Centre for Infection Research, Braunschweig (Germany)
German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: German Research Foundation (DFG); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725; AC52-07NA27344

OSTI ID:: 1630555

Alternate ID(s):: OSTI ID: 1043977

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 3; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (19)

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains Yarza, Pablo; Richter, Michael; Peplies, Jörg Systematic and Applied Microbiology, Vol. 31, Issue 4 https://doi.org/10.1016/j.syapm.2008.07.001	journal	September 2008
En route to a genome-based classification of Archaea and Bacteria? Klenk, H. -P.; Göker, M. Systematic and Applied Microbiology, Vol. 33, Issue 4 https://doi.org/10.1016/j.syapm.2010.03.003	journal	June 2010
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
Multiple sequence alignment using partial order graphs Lee, C.; Grasso, C.; Sharlow, M. F. Bioinformatics, Vol. 18, Issue 3 https://doi.org/10.1093/bioinformatics/18.3.452	journal	March 2002
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a New Anaerobic, Slightly Halophilic, Thiosulfate-Reducing Bacterium from Corroding Offshore Oil Wells Magot, M.; Ravot, G.; Campaignolle, X. International Journal of Systematic Bacteriology, Vol. 47, Issue 3 https://doi.org/10.1099/00207713-47-3-818	journal	July 1997
Dethiosulfovibrio russensis sp. nov., Dethosulfovibrio marinus sp. nov. and Dethosulfovibrio acidaminovorans sp. nov., novel anaerobic, thiosulfate- and sulfur-reducing bacteria isolated from 'Thiodendron' sulfur mats in different saline environments. Surkov, A. V.; Dubinina, G. A.; Lysenko, A. M. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 2 https://doi.org/10.1099/00207713-51-2-327	journal	March 2001
Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes' Jumas-Bilak, E.; Roudiere, L.; Marchandin, H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 5 https://doi.org/10.1099/ijs.0.006718-0	journal	April 2009
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences Kim, Byung Kwon; Lim, Young-Woon; Kim, Myungjin International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 10 https://doi.org/10.1099/ijs.0.64915-0	journal	October 2007
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T) Chovatia, Mansi; Sikorski, Johannes; Schröder, Maren Standards in Genomic Sciences, Vol. 1, Issue 3 https://doi.org/10.4056/sigs.40645	journal	November 2009
Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T) Chertkov, Olga; Sikorski, Johannes; Brambilla, Evelyne Standards in Genomic Sciences, Vol. 2, Issue 3 https://doi.org/10.4056/sigs.902116	journal	June 2010

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59 BASIC BIOLOGICAL SCIENCES
GEBA
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Synergistaceae
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anaerobic
motile
peptide utilization
thiosulfate-reducing
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Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)

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References (19)

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