Complete genome sequence of Thermaerobacter marianensis type strain (7p75a T)

Standards in Genomic Sciences

Volumn 3, Issue 3, 2010, Pages 337-345

  Han, Cliff ^a,b   Gu, Wei ^a,b   Zhang, Xiaojing ^a,b   Lapidus, Alla ^a   Nolan, Matt ^a   Copeland, Alex ^a   Lucas, Susan ^a   del Rio, Tijana Glavina ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Tapia, Roxane ^a,b   Goodwin, Lynne ^a,b   Pitluck, Sam ^a   Pagani, Ioanna ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Pati, Amrita ^a   Chen, Amy ^c   Palaniappan, Krishna ^c   Land, Miriam ^a,d   Hauser, Loren ^a,d   Chang, Yun Juan ^a,d   Jeffries, Cynthia D ^a,d   Schneider, Susanne ^e   Rohde, Manfred ^f   Göker, Markus ^e   Pukall, Rüdiger ^e   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^c   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^e   Detter, John C ^a,b   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chemoheterotrophic; Clostridiales; Deep sea; Family incertae sedis XVII; GEBA; Gram variable; None motile; Strictly aerobic; Thermophilic

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CLOSTRIDIALES; FIRMICUTES; THERMAEROBACTER; THERMAEROBACTER MARIANENSIS;

EID: 80053454597     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1373474     Document Type: Article

References (43)

1. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.
2. Takai K, Inoue A, Horikoshi K. Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11,000 m deep Mariana Trench. Int J Syst Bacteriol 1999; 49:619-628. PubMed doi:10.1099/00207713-49-2-619
3. Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590-592. PubMed doi:10.1099/00207713-47-2-590
4. Nunoura T, Akihara S, Takai K, Sako Y. Thermaerobacter nagasakiensis sp. nov., a novel aerobic and extremely thermophilic marine bacterium. Arch Microbiol 2002; 177:339-344. PubMed doi:10.1007/s00203-002-0398-2
5. Spanevello MD, Yamamoto H, Patel BK. Thermaerobacter subterraneus sp. nov., a novel aerobic bacterium from the Great Artesian Basin of Australia, and emendation of the genus Thermaerobacter. Int J Syst Evol Microbiol 2002; 52:795-800. PubMed doi:10.1099/ijs.0.01959-0
6. Tanaka R, Kawaichi S, Nishimura H, Sako Y. Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field. Int J Syst Evol Microbiol 2006;56:1531-1534. PubMed doi:10.1099/ijs.0.64203-0
7. Yabe S, Kato A, Hazaka M, Yokota A. Thermaerobacter composti sp. nov., a novel extremely thermophilic bacterium isolated from compost. J Gen Appl Microbiol 2009; 55:323-328. PubMed doi:10.2323/jgam.55.323
8. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259-2261. PubMed doi:10.1099/ijs.0.64915-0
9. Moriya T, Hikota T, Yumoto I, Ito T, Terui Y, Yamagishi A, Oshima T. Calditerricola satsumensis gen. nov., sp. nov. and C. yamamurae sp. nov., extreme thermophiles isolated from a high temperature compost. Int J Syst Bacteriol 2010 [Epub ahead of print] April 16 2010.
10. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JAE. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812-826. PubMed doi:10.1099/00207713-44-4-812
11. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 2007; 5:e77. PubMed doi:10.1371/journal.pbio.0050077
12. 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 Compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi:10.1128/AEM.03006-05
13. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
14. 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
15. 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
16. 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:10.1007/978-3-64202008-7_13
17. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2009; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
18. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
19. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
20. nd ed, vol.3. Springer, New York.
21. Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1-6. doi:10.1099/00207713-28-1-1
22. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
23. List Editor. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472. doi:10.1099/ijs.0.022855-0
24. Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.
25. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. doi:10.1099/0020771330-1-225
26. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
27. Notification List. Notification that new names and new combinations have appeared in volume 49, part 2, of the IJSB. Int J Syst Bacteriol 1999; 49:937-939. doi:10.1099/00207713-49-3-937
28. Classification of Bacteria and Archaea in risk groups. www.baua.de TRBA 466
29. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
30. Hamana K, Niitsu M, Samejima K, Itoh T. Polyamines of the thermophilic eubacteria belonging to the genera Thermosipho, Thermaerobacter and Caldicellulosiruptor. Microbios 2001; 104:177-185. PubMed
31. Hosoya R, Hamana K, Niitsu M, Itoh T. Polyamine analysis for chemotaxonomy of thermophilic eubacteria: Polyamine distribution profiles within the orders Aquificales, Thermotogales, Thermodesulfobacteriales, Thermales, Thermoanaerobacteriales, Clostridiales and Bacillales. J Gen Appl Microbiol 2004; 50:271-287. PubMed doi:10.2323/jgam.50.271
32. Klenk HP, Goeker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed doi:10.1016/j.syapm.2010.03.003
33. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed doi:10.1038/nature08656
34. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475-D479. PubMed doi:10.1093/nar/gkm884
35. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
36. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed doi:10.1101/gr.074492.107
37. T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
38. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
39. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
40. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
41. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393
42. DOE Joint Genome Institute. http://www.jgi.doe.gov.
43. The Pred/Phrap/Consed software package. http://www.phrap.com.