Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P T)

Standards in Genomic Sciences

Volumn 3, Issue 2, 2010, Pages 108-116

  Pitluck, Sam ^a   Yasawong, Montri ^b   Munk, Christine ^a,c   Nolan, Matt ^a   Lapidus, Alla ^a   Lucas, Susan ^a   del Rio, Tijana Glavina ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Bruce, David ^a,c   Detter, Chris ^a,c   Tapia, Roxanne ^a,c   Han, Cliff ^a,c   Goodwin, Lynne ^a,c   Liolios, Konstantinos ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Pati, Amrita ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,e   Chang, Yun Juan ^a,e   Jeffries, Cynthia D ^a,e   Rohde, Manfred ^b   Spring, Stefan ^f   Sikorski, Johannes ^f   Göker, Markus ^f   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^d   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^f   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

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

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Anaerobe; Barophile; Chemoorganotroph; Core sample; Deep sea sediment; Firmicutes; GEBA; Thermoanaerobacterales; Thermophile; Upwelling system

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); FIRMICUTES; NEGIBACTERIA; THERMOSEDIMINIBACTER; THERMOSEDIMINIBACTER OCEANI;

EID: 80053344181     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1133078     Document Type: Article

References (32)

1. Lee YJ, Wagner ID, Brice ME, Kevbrin VV, Mills GL, Romanek CS, Wiegel J. Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin. Extremophiles 2005; 9:375-383. PubMed doi:10.1007/s00792-005-0453-4
2. Validation list no. 132. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2010; 60:469-472. doi:10.1099/ijs.0.022855-0
3. Wiegel J. 2009. Family I. Thermoanaerobacteraceae fam. nov., p. 1225. In P De Vos, GM Garrity, D.Jones, NR Krieg, W Ludwig, FA Rainey, KH Schleifer, and W Whitman (eds), Bergey's Manual of Systematic Bacteriology, second ed, vol. 3. Springer-Verlag, New York.
4. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.
5. Validation list no. 109. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:925-927. PubMed doi:10.1099/ijs.0.64380-0
6. 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
7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2009; 37:D26-D31. PubMed doi:10.1093/nar/gkn723
8. Nazina TN, Shestakova NM, Grigor'ian AA, Mikhailova EM, Turova TP, Poltaraus AB, Feng C, Ni F, Beliaev SS. Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang Oilfield (China). Mikrobiologiia 2006; 75:70-81. PubMed
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
10. 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
11. 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
12. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló- Móra R. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all se- quenced type strains. Syst Appl Microbiol 2008; 31:241-250. PubMed doi:10.1016/j.syapm.2008.07.001
13. 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
14. 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 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
15. 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
16. 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
17. Garrity GM, Holt JG. 2001. The Road Map to the Manual, p. 119-169. In G. M. Garrity, D. R. Boone, and R. W. Castenholz (ed.), Bergey's Manual of Systematic Bacteriology, 2 ed, vol. 1. Springer, New York.
18. Gibbons NE, Murrey RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 1978; 28:1-6. doi:10.1099/00207713-28-1-1
19. Rainey FA. 2009. Class II. Clostridia class nov, p. 736. In: P De Vos, GM Garrity, D Jones, NR Krieg, W Ludwig, FA Rainey, KH Schleifer, W Whitman (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 3 (The Firmicutes), vol. 3. Springer, Dordrecht, Heidelberg, London, New York.
20. Wiegel J. Order III. Thermoanaerobacterales ord. 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, SpringerVerlag, New York, 2009, p. 1224.
21. Classification of bacteria and archaea in risk groups. TRBA 466.
22. D'Hondt SL, Jørgensen BB, Miller DJ, Aiello IW, Bekins B, Blake R, Cragg BR, Cypionka H, Dickens GR, Ferdelman T, et al. Init Repts, 201: College Station, TX (Ocean Drilling Program) 2003.
23. 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
24. Klenk HP, Göker 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
25. 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
26. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
27. 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
28. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. HR Arabnia & H Valafar (eds), CSREA Press. June 26-29, 2006; 141-146.
29. 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.
30. 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
31. 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
32. 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