Complete genome sequence of Sanguibacter keddieii type strain (ST-74 T)

Standards in Genomic Sciences

Volumn 1, Issue 2, 2009, Pages 110-118

  Ivanova, Natalia ^a   Sikorski, Johannes ^b   Sims, David ^a   Brettin, Thomas ^a,c   Detter, John C ^a,c   Han, Cliff ^a,c   Lapidus, Alla ^a   Copeland, Alex ^a   del Rio, Tijana Glavina ^a   Nolan, Matt ^a   Chen, Feng ^a   Lucas, Susan ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Bruce, David ^a,c   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Pati, Amrita ^a   Mavromatis, Konstantinos ^a   Chen, Amy ^d   Palaniappan, Krishna ^d   D'haeseleer, Patrik ^a,e   Chain, Patrick ^a,e   Bristow, Jim ^a   Eisen, Jonathan A ^a,f   Markowitz, Victor ^d   Hugenholtz, Philip ^a   Göker, Markus ^b   Pukall, Rüdiger ^b   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 LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Aerobic; Blood isolate; Facultative anaerobic; Micrococcineae; Sanguibacteraceae

Indexed keywords

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); CELLULOMONADACEAE; MICROCOCCINEAE; OERSKOVIA; SANGUIBACTER; SANGUIBACTER KEDDIEII; SANGUIBACTERACEAE;

EID: 80053348757     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.16197     Document Type: Article

References (31)

1. Fernández-Garayzábal JF, Dominguez L, Pascual C, Jones D, Collins MD. Phenotypic and phylogenetic characterization of some unknown coryneform bacteria isolated from bovine blood and milk: description of Sanguibacter gen.nov. Lett Appl Microbiol 1995; 20:69-75. pubMed doi:10.1111/j.1472-765X.1995.tb01289.x
2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479-491.
3. Prauser H, Lechevalier MP, Lechevalier HA. Description of Oerskovia gen. nov. to harbor Oerskov's motile Nocardia. Appl Microbiol 1970; 19:534. pubMed
4. Pascual C, Collins MD, Grimont PAD, Domin-guez L, Fernandes-Garayzabal JF. Sanguibacter inulinus sp. nov. Int J Syst Bacteriol 1996; 46:811-813. pubMed
5. Huang Y, Dai X, He L, Wang YN, Wang BJ, Liu Z, Liu SJ. Sanguibacter marinus sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2005; 55:1755-1758. pubMed doi:10.1099/ijs.0.63471-0
6. Kim MK, Pulla RK, Kim SY, Yi TH, Soung NK, Yang DC. Sanguibacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008; 58:538-541. pubMed doi:10.1099/ijs.0.65399-0
7. Hong SG, Lee YK, Yim JH, Chun J, Lee HK. Sanguibacter antarcticus sp. nov., isolated from An-arctic sea sand. Int J Syst Evol Microbiol 2008; 58:50-52. pubMed doi:10.1099/ijs.0.65031-0
8. 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
9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368-376. pubMed doi:10.1007/BF01734359
10. 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
11. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes OnLine 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
12. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angi-uoli SV, et al. Towards a richer description of our complete collection of genomes and metage-nomes: the "Minimum Information about a Ge-nome Sequence" (MIGS) specification. Nat Bio-technol 2008; 26:541-547. pubMed doi:10.1038/nbt1360
13. Garrity GM, Holt J. Taxonomic Outline of the Archaea and Bacteria. Bergey's Manual of Syste-matic Bacteriology, 2nd Ed. In: G.Garrity GM, Boone DR, Castenholz RW Eds. Vol 1 The Arc-haea, Deeply Branching and Phototrophic Bacteria. 2001 pp. 155-166
14. 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
15. Stackebrandt E, Schumann P. Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae. Int J Syst Evol Microbiol 2000; 50:1279-1285. pubMed
16. Anonymous Biological Agents. Technical rules for biological agents www.baua.de TRBA 466.
17. Ashburner M, Ball CA, Blake JA, Botstein D, But-ler 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 doi:10.1038/75556
18. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia ad related taxa. J Appl Bacteriol 1979; 47:87-89.
19. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
20. Wu M, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 2009; (In press).
21. Han CS, Chain P. 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.
22. Besemer J, Lomsadze A, Borodovsky M. Gene-MarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607-2618. pubMed doi:10.1093/nar/29.12.2607
23. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. Expert IMG ER: A system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. pubMed doi:10.1093/bioinformatics/btp393
24. Pati A, Ivanova N, Mikhailova, N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted)
25. 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 doi:10.1093/nar/25.5.955
26. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108. pubMed doi:10.1093/nar/gkm160
27. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005; 33:D121-D124. pubMed doi:10.1093/nar/gki081
28. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IMA, Dubchak I, Anderson I, Ly-kidis A, Mavromatis K, et al. The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 2008; 36:D528-D533. pubMed doi:10.1093/nar/gkm846
29. Karp PD, Paley SM, Romero P. The Pathway Tools Software. Bioinformatics 2002; 18:S225-S232. pubMed
30. Caspi R, Karp P, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley SM, Rhee SY, Shearer A, et al. The MetaCyc Database of metabolic pathways and enzymes and the Bio-Cyc collection of pathway/Genome Databases. Nucleic Acids Res 2008; 36:D623-D631. pubMed doi:10.1093/nar/gkm900
31. Karp PD, Ouzounis CA, Moore-Kochlacs C, Gol-dovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005; 33:6083-6089. pubMed doi:10.1093/nar/gki892