Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)

Standards in Genomic Sciences

Volumn 6, Issue 2, 2012, Pages 155-164

  Anderson, Iain ^a   Saunders, Elizabeth ^a,b   Lapidus, Alla ^a   Nolan, Matt ^a   Lucas, Susan ^a   Tice, Hope ^a   Del Rio, Tijana Glavina ^a   Cheng, Jan Fang ^a   Han, Cliff ^a,b   Tapia, Roxanne ^a,b   Goodwin, Lynne A ^a,b   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Mavromatis, Konstantinos ^a   Pagani, Ioanna ^a   Ivanova, Natalia ^a   Mikhailova, Natalia ^a   Pati, Amrita ^a   Chen, Amy ^c   Palaniappan, Krishna ^c   Land, Miriam ^a,d   Hauser, Loren ^a,d   Jeffries, Cynthia D ^a,d   Chang, Yun Juan ^a,d   Brambilla, Evelyne Marie ^f   Rohde, Manfred ^e   Spring, Stefan ^f   Göker, Markus ^f   Detter, John C ^a,b   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^c   Hugenholtz, Philip ^a,h   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^f   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 HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

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

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Black smoker; Chemolithoautotrophic; GEBA; Gram negative; Motile; Strictly anaerobic; Sulfate reducing; Thermodesulfobacteria; Thermodesulfobacteriaceae; Thermophilic

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CHEMOTAXONOMY; CLASSIFICATION; GENE SEQUENCE; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; RNA GENE; SCANNING ELECTRON MICROSCOPY; SULFATE REDUCING BACTERIUM; THERMODESULFATATOR INDICUS;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; THERMODESULFATATOR INDICUS; THERMODESULFOBACTERIA; THERMODESULFOBACTERIACEAE;

EID: 84863575494     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2665915     Document Type: Article

References (37)

1. Moussard H, L'Haridon S, Tindall BJ, Banta A, Schumann P, Stackebrandt E, Reysenbach AL, Jeanthon C. Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 2004; 54:227-233. PubMed http://dx.doi.org/10.1099/ijs.0.02669-0
2. Alain K, Postec A, Grinsard E, Lesongeur F, Prieur D, Godfroy A. Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent. Int J Syst Evol Microbiol 2010; 60:33-38. PubMed http://dx.doi.org/10.1099/ijs.0.009449-0
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
4. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebastopol, 2003.
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 compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed http://dx.doi.org/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 http://dx.doi.org/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 http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
9. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
10. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
11. 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. http://dx.doi.org/10.1007/978-3-642-02008-7_13
12. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
13. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, 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 http://dx.doi.org/10.1093/nar/gkp848
14. 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 http://dx.doi.org/10.1038/nbt1360
15. 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 http://dx.doi.org/10.1073/pnas.87.12.4576
16. Garrity GM, Holt JG. Phylum BIII. Thermodesulfobacteria phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 389.
17. List Editor. Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2002; 52:685-690. PubMed http://dx.doi.org/10.1099/ijs.0.02358-0
18. Hatchikian EC, Ollivier B, Garcia JL. Class I. Thermodesulfobacteria class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 389.
19. Hatchikian EC, Ollivier B, Garcia JL. Order I. Thermodesulfobacteriales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 389.
20. Hatchikian EC, Ollivier B, Garcia JL. Family I. Thermodesulfobacteriaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second edition, Volume 1, Springer, New York, 2001, p. 390.
21. BAuA. 2010, Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 466, p. 235.
22. 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. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
23. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/10.1016/j.syapm.2010.03.003
24. 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 http://dx.doi.org/10.1038/nature08656
25. List of growth media used at DSMZ. http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technolog y/list-of-media-for-microorganisms.html.
26. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank 2011; 9:51-55. http://dx.doi.org/10.1089/bio.2010.0029
27. The DOE Joint Genome Institute. http://www.jgi.doe.gov
28. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
29. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
30. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26-29, 2006: 141-146.
31. 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 http://dx.doi.org/10.1186/1471-2105-11-119
32. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods 2010; 7:455-457. PubMed http://dx.doi.org/10.1038/nmeth.1457
33. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed
34. Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 2007; 35:3100-3108. PubMed http://dx.doi.org/10.1093/nar/gkm160
35. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003; 31:439-441. PubMed http://dx.doi.org/10.1093/nar/gkg006
36. 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 http://dx.doi.org/10.1006/jmbi.2000.4315
37. 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 http://dx.doi.org/10.1016/j.jmb.2004.05.028