Complete genome sequence of Tolumonas auensis type strain (TA 4T)

Standards in Genomic Sciences

Volumn 5, Issue 1, 2011, Pages 112-120

  Chertkov, Olga ^a,b   Copeland, Alex ^a   Lucas, Susan ^a   Lapidus, Alla ^a   Berry, Kerrie W ^a   Detter, John C ^a,b   del Rio, Tijana Glavina ^a   Hammon, Nancy ^a   Dalin, Eileen ^a   Tice, Hope ^a   Pitluck, Sam ^a   Richardson, Paul ^a   Bruce, David ^a,b   Goodwin, Lynne ^a,b   Han, Cliff ^a,b   Tapia, Roxanne ^a,b   Saunders, Elizabeth ^a,b   Schmutz, Jeremy ^b   Brettin, Thomas ^a,c   Larimer, Frank ^a,c   Land, Miriam ^a,c   Hauser, Loren ^a,c   Spring, Stefan ^d   Rohde, Manfred ^e   Kyrpides, Nikos C ^a   Ivanova, Natalia ^a   Göker, Markus ^d   Beller, Harry R ^f   Klenk, Hans Peter ^d   Woyke, Tanja ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

^d DSMZ German Collection of Microorganisms and Cell Cultures ^*  (United Kingdom)

^e HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Aeromonadaceae; Chemoorganotrophic; Facultatively anaerobic; Gammaproteobacteria; Gram negative; JBEI 2008; Non motile; Toluene producer

Indexed keywords

AEROMONADACEAE; AEROMONAS HYDROPHILA; AEROMONAS HYDROPHILA SUBSP. HYDROPHILA; GAMMAPROTEOBACTERIA; NEGIBACTERIA; TOLUMONAS; TOLUMONAS AUENSIS;

EID: 80054951249     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2184986     Document Type: Article

References (34)

1. Fischer-Romero C, Tindall BJ, Jüttner F. Tolumo-nas auensis gen. nov., sp. nov., a toluene-producing bacterium from anoxic sediments of a freshwater lake. Int J Syst Bacteriol 1996; 46:183-188. PubMed doi:10.1099/00207713-46-1-183
2. Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Inter-net. Int J Syst Bacteriol 1997; 47:590-592. PubMed doi:10.1099/00207713-47-2-590
3. Caldwell ME, Allen TD, Lawson PA, Tanner RS. Tolumonas osonensis sp. nov., isolated from anoxic freshwater sediment. Int J Syst Bacteriol Dec 2010 Epub ahead of print PMID: 21148672.
4. Altschul SF, Gish W, Miller W, Myers EW, Lip-man DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
5. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compat-ible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi:10.1128/AEM.03006-05
6. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
7. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
9. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758-771. PubMed doi:10.1080/10635150802429642
10. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184-200.doi:10.1007/978-3-642-02008-7_13
11. Swofford DL. PAUP*: Phylogenetic Analysis Us-ing Parsimony (*and other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
12. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Kyrpides NC. The genomes on line database (GOLD) in 2009: Status of genomic and metage-nomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
13. Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, et al. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J Bacteriol 2006; 188:8272-8282. PubMed doi:10.1128/JB.00621-06
14. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, An-giuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
15. Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
16. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms. Proposal for the do-mains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
17. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Pro-teobacteria phyl. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteo-bacteria), Springer, New York, 2005, p. 1.
18. Garrity GM, Bell JA, Lilburn T. Class III. Gamma-proteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
19. Validation List 106. Int J Syst Evol Microbiol 2005; 55:2235-2238.doi:10.1099/ijs.0.64108-0
20. Martin-Carnahan A, Joseph SW. Order XII. Aero-monadales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Sys-tematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 556.
21. Colwell RR, Macdonell MT, De Ley J. Proposal to recognize the family Aeromonadaceae fam. nov. Int J Syst Bacteriol 1986; 36:473-477. doi:10.1099/00207713-36-3-473
22. BAuA. Classification of bacteria and archaea in risk groups. TRBA 2005; 466:348.
23. Ashburner M, Ball CA, Blake JA, Botstein D, But-ler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the un-ification of biology. The Gene Ontology Consor-tium. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
24. List of growth media used at DSMZ: http//www.dsmz.de/microorganisms/media_list.php.
25. The DOE Joint Genome Institute. http://www.jgi.doe.gov
26. Phrap and Phred for Windows, MacOS, Linux, and Unix. http://www.phrap.com
27. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. PubMed doi:10.4056/sigs.761
28. Hyatt D, Chen GL, Locascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal Prokaryotic Dynam-ic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119.PubMed doi:10.1186/1471-2105-11-119
29. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for mi-crobial genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
30. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in ge-nomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed doi:10.1093/nar/25.5.955
31. Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent an-notation of rRNA genes in genomic sequences. Nucleic Acids Res 2007; 35:3100-3108. PubMed doi:10.1093/nar/gkm160
32. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003; 31:439-441. PubMed doi:10.1093/nar/gkg006
33. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 2001; 305:567-580. PubMed doi:10.1006/jmbi.2000.4315
34. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795. PubMed doi:10.1016/j.jmb.2004.05.028