Complete genome sequence of Truepera radiovictrix type strain (RQ-24 T)

Standards in Genomic Sciences

Volumn 4, Issue 1, 2011, Pages 91-96

  Ivanova, Natalia ^a   Rohde, Christine ^b   Munk, Christine ^a,c   Nolan, Matt ^a   Lucas, Susan ^a   del Rio, Tijana Glavina ^a   Tice, Hope ^a   Deshpande, Shweta ^a   Cheng, Jan Fang ^a   Tapia, Roxane ^a,c   Han, Cliff ^a,c   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Liolios, Konstantinos ^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   Brambilla, Evelyne ^b   Rohde, Manfred ^f   Göker, Markus ^f   Tindall, Brian J ^b   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^d   Hugenholtz, Philip ^a,h   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^b   Lapidus, Alla ^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

Aerobic; Alkaliphilic; Chemoorganotrophic; Facultatively halophilic; GEBA; Gram indeterminate; Non motile; Radiation resistant; Spherical shaped; Thermophilic; Trueperaceae

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); DEINOCOCCALES; DEINOCOCCUS; TRUEPERA; TRUEPERA RADIOVICTRIX; TRUEPERACEAE;

EID: 80053341990     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1563919     Document Type: Article

References (38)

1. Albuquerque L, Simoes C, Nobre MF, Pino NM, Battista JR, Silva MT, Rainey FA, Da Costa MS. Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Tru-eperaceae fam. nov. FEMS Microbiol Lett 2005; 247:161-169. PubMed doi:10.1016/j.femsle.2005.05.002
2. Euzéby J. Validation of publication of new names and new combinations previously effectively pub-lished outside the IJSEM. Int J Syst Evol Microbiol 2005; 55:1743-1745. PubMed doi:10.1099/ijs.0.63996-0
3. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
4. 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
5. 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
6. 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
7. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: sta-tus of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
8. de Groot A, Dulermo R, Ortet P, Blanchard L, Guerin P, Fernandez B, Vacherie B, Dossat C, Joli-vet E, Siguier P, et al. Alliance of proteomics and genomics to unravel the specificities of Sahara bac-terium Deinococcus deserti. PLoS Genet 2009; 5:e1000434. PubMed doi:10.1371/journal.pgen.1000434
9. Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, et al. Deinococcus geothermalis: the pool of extreme radiation resis-tance genes shrinks. PLoS ONE 2007; 2:e955. PubMed doi:10.1371/journal.pone.0000955
10. Pukall R, Zeytun A, Lucas A, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF, Pitluck S, Liolios K, et al. Complete genome sequence of Deinococcus maricopensis type strain (LB-34T). Stand Genomic Sci 2011; (next issue).
11. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiothermus ruber type strain (21T). Stand Genom-ic Sci 2010; 3:26-36. PubMed doi:10.4056/sigs.1032748
12. White O, Eisen JA, Heidelberg JF, Hickey EK, Pe-terson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, et al. Genome sequence of the radioresistant bacterium Deinococcus radiodu-rans R1. Science 1999; 286:1571-1577. PubMed doi:10.1126/science.286.5444.1571
13. White O, Eisen JA, Heidelberg JF, Hickey EK, Pe-terson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, et al. Erratum: Genome se-quence of the radioresistant bacterium Deinococ-cus radiodurans R1. Science 2004; 303:1571-1577.
14. de Santis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, An-dersen 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
15. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137. doi:10.1108/eb046814
16. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuo-li SV, et al. The minimum information about a ge-nome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
18. Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construc-tion. Syst Appl Microbiol 1989; 11:128-134. PubMed
19. Garrity GM, Holt JG. 2001. Taxonomic outline of the Archaea and Bacteria, p. 155-166. In G. M. Garrity, D. R. Boone, and R. W. Castenholz (ed.), Bergey's Manual of Systematic Bacteriology, 2nd ed, vol. 1. Springer, New York.
20. 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
21. Garrity GM, Holt JG. Class I. Deinococci 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. 395.
22. Rainey FA, Nobre MF, Schumann P, Stackebrandt E, da Costa MS. Phylogenetic diversity of the dei-nococci as determined by 16S ribosomal DNA se-quence comparison. Int J Syst Bacteriol 1997; 47:510-514. PubMed doi:10.1099/00207713-47-2-510
23. Classification of bacteria and archaea in risk groups. http://www.baua.deTRBA466.
24. 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 unifica-tion of biology. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
25. Ferreira AC, Nobre MF, Moore E, Rainey FA, Bat-tista JR, da Costa MS. Characterization and radia-tion resistance of new isolates of Rubrobacter radi-otolerans and Rubrobacter xylanophilus. Extremo-philes 1999; 3:235-238. PubMed doi:10.1007/s007920050121
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, Da-lin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic en-cyclopaedia 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. 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 Bio-banking (In press).
30. DNA bank Network. http://www.dnabank-network.org
31. The DOE Joint Genome Institute. http://www.jgi.doe.gov
32. Phrap and Phred for Windows, MacOS, Linux, and Unix. http://www.phrap.com
33. 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
34. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Ky-tococcus sedentarius type strain (541T). Stand Ge-nomic Sci 2009; 1:12-20. PubMed doi:10.4056/sigs.761
35. 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.
36. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recogni-tion and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
37. 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
38. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393