Complete genome sequence of Vulcanisaeta distributa type strain (IC-017 T)

Standards in Genomic Sciences

Volumn 3, Issue 2, 2010, Pages 117-125

  Mavromatis, Konstantinos ^a   Sikorski, Johannes ^b   Pabst, Elke ^c   Teshima, Hazuki ^a,d   Lapidus, Alla ^a   Lucas, Susan ^a   Nolan, Matt ^a   del Rio, Tijana Glavina ^a   Cheng, Jan Fang ^a   Bruce, David ^a,d   Goodwin, Lynne ^a,d   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Ivanova, Natalia ^a   Mikhailova, Natalia ^a   Pati, Amrita ^a   Chen, Amy ^e   Palaniappan, Krishna ^a   Land, Miriam ^a,f   Hauser, Loren ^a,f   Chang, Yun Juan ^a,f   Jeffries, Cynthia D ^a,f   Rohde, Manfred ^g   Spring, Stefan ^b   Göker, Markus ^b   Wirth, Reinhard ^c   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,h   Markowitz, Victor ^a   Hugenholtz, Philip ^a   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 UNIVERSITY OF REGENSBURG   (Germany)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f OAK RIDGE NATIONAL LABORATORY   (United States)

^g HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Acidophilic; Crenarchaeota; GEBA; Hyperthermophilic; Microaerotolerant anaerobe; Non motile; Thermoproteaceae

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; THERMOPROTEACEAE; VULCANISAETA; VULCANISAETA DISTRIBUTA;

EID: 79955542242     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1113067     Document Type: Article

References (33)

1. Itoh T, Suzuki K, Nakase T. Vulcanisaeta distributa gen. nov., sp. nov., and Vulcanisaeta souniana sp. nov., novel hyperthermophilic, rodshaped crenarchaeotes isolated from hot springs in Japan. Int J Syst Evol Microbiol 2002; 52:1097-1104. PubMed doi:10.1099/ijs.0.02152-0
2. Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the In ternet. Int J Syst Bacteriol 1997; 47:590-592. PubMed doi:10.1099/00207713-47-2-590
3. Kimura H, Ishibashi JI, Masuda H, Kato K, Hanada S. Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere. Appl Environ Microbiol 2007; 73:2110-2117. PubMed doi:10.1128/AEM.02800-06
4. Itoh T, Nomura N, Sako Y. Distribution of 16S rRNA introns among the family Thermoproteaceae and their evolutionary implications. Extremophiles 2003; 7:229-233. PubMed
5. 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
6. 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
7. Garrity GM, Holt JG. 2001. Phylum AI. Crenarchaeota phy. nov., p. 169-210. In GM Garrity, DR Boone, and RW Castenholz (eds.), Bergey's Manual of Systematic Bacteriology, second edition ed, vol. 1. Springer, New York.
8. 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 doi:10.1099/ijs.0.02358-0
9. Reysenbach AL. 2001. Class I. Thermoprotei class. nov., p. 169. In GM Garrity, DR Boone, RW Castenholz (eds), Bergey's Manual of Systematic Bacteriology, second edition ed, vol. 1. Springer, New York.
10. Zillig W, Stetter KO, Schäfer W, Janekovic D, Wunderl S, Holz J, Palm P. Thermoproteales: a novel type of extremely thermoacidophilic anaerobic archaebacteria isolated from Icelandic solfataras. Zentralbl Bakteriol Hyg 1. Abt Orig C 1981; 2:205-227.
11. Judicial Commission of the International Committee on Systematics of Prokaryotes. The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplas ma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518. PubMed doi:10.1099/ijs.0.63548-0
12. Burggraf S, Huber H, Stetter KO. Reclassification of the crenarchaeal orders and families in accordance with 16S rRNA sequence data. Int J Syst Bacteriol 1997; 47:657-660. PubMed doi:10.1099/00207713-47-3-657
13. List editor. Validation of the publication of new names and new combinations previously effectively published outside the IJSB: List No. 8. Int J Syst Bacteriol 1982; 32:266-268. oi:10.1099/00207713-32-2-266
14. Classification of bacteria and archaea in risk groups. TRBA 466.
15. 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
16. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
17. 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
18. 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
19. 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
20. 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
21. Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, et al. Complete genome sequence of an aerobic hyper-thermophilic cre narchaeon, Aeropyrum pernix K1. DNA Res 1999; 6:83-101, 145-152. PubMed doi:10.1093/dnares/6.2.83
22. Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP. The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. Archaea 2006; 2:127-135. PubMed doi:10.1155/2007/745987
23. Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, et al. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics 2009; 10:145. PubMed doi:10.1186/1471-2164-10145
24. T). Stand Genomic Sci 2010; 2:245-259. doi:10.4056/sigs.821804
25. Hamana K, Tanaka T, Hosoya R, Niitsu M, Itoh T. Cellular polyamines of the acidophilic, thermophilic and thermoacidophilic archaebacteria, Acidilobus, Ferroplasma, Pyrobaculum, Pyrococcus, Staphylothermus, Thermococcus, Thermodiscus and Vulcanisaeta. J Gen Appl Microbiol 2003; 49:287-293. PubMed doi:10.2323/jgam.49.287
26. 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
27. 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
28. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
29. Cliff S. Han, Patrick Chain. 2006. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Hamid R Arabnia & Homayoun Valafar (eds), CSREA Press. June 26-29, 2006: 141-146.
30. T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
31. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
32. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene PRIMP: A gene prediction improvement pipeline for microbial 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. Bioinformatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393