Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1 T)

Standards in Genomic Sciences

Volumn 4, Issue 3, 2011, Pages 322-330

  Anderson, Iain ^a   Sikorski, Johannes ^b   Zeytun, Ahmet ^a,c   Nolan, Matt ^a   Lapidus, Alla ^a   Lucas, Susan ^a   Hammon, Nancy ^a   Deshpande, Shweta ^a   Cheng, Jan Fang ^a   Tapia, Roxanne ^a,c   Han, Cliff ^a,c   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Pagani, Ioanna ^a   Ivanova, Natalia ^a   Huntemann, Marcel ^a   Mavromatis, Konstantinos ^a   Ovchinikova, Galina ^a   Pati, Amrita ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,e   Brambilla, Evelyne Marie ^b   Ngatchou Djao, Olivier D ^f   Rohde, Manfred ^f   Tindall, Brian J ^b   Göker, Markus ^b   Detter, John C ^a,c   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^d   Hugenholtz, Philip ^a,h   Klenk, Hans Peter ^b   Kyrpides, Nikos C ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

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

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Anaerobic; GEBA; Gram negative; Mesophilic; Microaerobic; Nautiliaceae; Non motile; Strictly chemo lithoautotroph

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EPSILONPROTEOBACTERIA; NAUTILIACEAE; NEGIBACTERIA; NITRATIFRACTOR; NITRATIFRACTOR SALSUGINIS;

EID: 80053376337     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1844518     Document Type: Article

References (33)

1. Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sa-ko Y. Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the ep-silon-Proteobacteria isolated from a deep-sea hy-drothermal system in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 2005; 55:925-933. PubMed doi:10.1099/ijs.0.63480-0
2. Takai K, Inagaki F, Nakagawa S, Hirayama H, Nunoura T, Sako Y, Nealson KH, Horikoshi K. Isolation and phylogenetic diversity of members of previously uncultivated ε-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol Lett 2003; 218:167-174. PubMed
3. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K, Huber T, Dalevi D, Hu P, Andersen G. 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
4. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems. 1980; 14:130-137.
5. Teske A, Hinrichs KU, Edgcomb VP, Gomez AD, Kysela DT, Sogin ML, Jannasch HW. Microbial diversity of hydrothermal sediments in the Guay-mas Basin: evidence for anaerobic methanotroph-ic communities. Appl Environ Microbiol 2002; 68:1994-2007. PubMed doi:10.1128/AEM.68.4.1994-2007.2002
6. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
7. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
8. 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
9. 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
10. 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
11. Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, et al. Adaptations to submarie hy-drothermal environments exemplified by the genome of Natilia profundicola. PLoS Genet 2009; 5:e1000362. PubMed doi:10.1371/journal.pgen.1000362
12. Yarza P, Ludwig W, Euzéby J, Amman R, Schlei-fer KH, Glöckner FO, Rosselló-Mora R. Updates of the All-Species-Living-Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010; 33:291-299. PubMed doi:10.1016/j.syapm.2010.08.001
13. 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
14. 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
15. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Pro-teobacteria phyl. 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.
16. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1-6. PubMed doi:10.1099/ijs.0.64188-0
17. Garrity GM, Bell JA, Lilburn T, Class V. Epsilon-proteobacteria class. nov. In: Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2 (The Pro-teobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), p. 1145. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garri-ty. New York: Springer. 2005.
18. Miroshnichenko ML, L'Haridon S, Schumann P, Spring S, Bonch-Osmolovskaya EA, Jeanthon C, Stackebrandt E. Caminibacter profundus sp. nov., a novel thermophile of Nautiliales ord. nov. within the class 'Epsilonproteobacteria', isolated from a deep-sea hydrothermal vent. Int J Syst Evol Mi-crobiol 2004; 54:41-45. PubMed doi:10.1099/ijs.0.02753-0
19. BAuA. Classification of bacteria and archaea in risk groups. TRBA 2010; 466:150.
20. 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
21. Takai K, Campbell BJ, Cary SC, Suzuki M, Oida H, Nunoura T, Hirayama H, Nakagawa S, Suzuki Y, Inagaki F, et al. Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria. Appl Environ Microbiol 2005; 71:7310-7320. PubMed doi:10.1128/AEM.71.11.7310-7320.2005
22. 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
23. 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
24. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
25. Gemeinholzer B, Dröge G, Zetzsche H, Haszpru-nar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51-55. doi:10.1089/bio.2010.0029
26. JGI website. http://www.jgi.doe.gov
27. The Phred/Phrap/Consed software package. http://www.phrap.com
28. 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
29. 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.
30. 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
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 doi:10.1186/1471-2105-11-119
32. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
33. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393