Complete genome sequence of Streptosporangium roseum type strain (NI 9100 T)

Standards in Genomic Sciences

Volumn 2, Issue 1, 2010, Pages 29-37

  Nolan, Matt ^a   Sikorski, Johannes ^b   Jando, Marlen ^b   Lucas, Susan ^a   Lapidus, Alla ^a   del Rio, Tijana Glavina ^a   Chen, Feng ^a   Tice, Hope ^a   Pitluck, Sam ^a   Cheng, Jan Fang ^a   Chertkov, Olga ^a,c   Sims, David ^a,c   Meincke, Linda ^a,c   Brettin, Thomas ^a,c   Han, Cliff ^a,c   Detter, John C ^a,c   Bruce, David ^a,c   Goodwin, Lynne ^a,c   Land, Miriam ^a,d   Hauser, Loren ^a,d   Chang, Yun Juan ^a,d   Jeffries, Cynthia D ^a,d   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Chen, Amy ^e   Palaniappan, Krishna ^e   Chain, Patrick ^a,c   Rohde, Manfred ^f   Göker, Markus ^b   Bristow, Jim ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^e   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^b   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 OAK RIDGE NATIONAL LABORATORY   (United States)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Aerobic; GEBA; Gram positive; Non motile; Non motile spores; S. claviforme; Sporangia; Streptosporangiaceae; Vegetative and aerial mycelia

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); MYCELIUM (GENUS); POSIBACTERIA; STREPTOMYCES; STREPTOSPORANGIACEAE; STREPTOSPORANGIUM; STREPTOSPORANGIUM CLAVIFORME; STREPTOSPORANGIUM ROSEUM;

EID: 80053347254     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.631049     Document Type: Article

References (33)

1. Stackebrandt E, Kroppenstedt RM, Jahnke KD, Kemmerling C, Gürtler H. Transfer of Streptosporangium viridogriseum (Okuda et al. 1966), Streptosporangium viridogriseum subsp. Kofuense (Nonomura and Ohara 1969), and Streptosporangium albidum (Furumai et al. 1968) to Kutzneria gen. nov. as Kutzneria viridogrisea comb. nov., Kutzneria kofuensis comb. nov., and Kutzneria albida comb. nov., respectively, and emendation of the Genus Streptosporangium. Int J Syst Bacteriol 1994; 44:265-269.
2. Couch JN. A new genus and family of the Actinomycetales, with a revision of the genus Actinoplanes. J Elisha Mitchell Sci Soc 1955; 71:148-155
3. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420
4. Couch JN, Bland CE. Genus III. Streptosporangium Couch 1955, 148. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 711-715
5. Nonomura H, Ohara Y. Distribution of the actinomycetes in soil. IV. The isolation and classificaBerkeley National Laboratory under contract No. DE- AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE- AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. tion of the genus Streptosporangium. J Ferment Technol 1960; 38:405-409
6. Petrolini B, Quaroni S, Sardi P, Saracchi M, Andriolollo N. A sporangiate actinomycete with unusual morphological features: Streptosporangium claviforme sp. nov. Actinomycetes 1992; 3:45-50
7. Ward-Rainey N, Rainey FA, Stackebrandt E. The phylogenetic structure of the genus Streptosporangium. Syst Appl Microbiol 1996; 19:50-55
8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552 PubMed
9. 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
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 On Line Database (GOLD) in 2007: status of genomic and metagenomic Streptosporangium roseum type strain (NI 9100T) projects and their associated metadata. Nucleic Acids Res 2008; 36:D475-D479. PubMeddoi:10.1093/nar/gkm884
12. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thompson N, Allen MJ, Anguiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMeddoi:10.1038/nbt1360
13. 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. PubMeddoi:10.1073/pnas.87.12.4576
14. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169
15. 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
16. Goodfellow M, Stanton LJ, Simpson KE, Minnikin DE. Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 1990; 136:19-36
17. List Editor. Validation List no. 34. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1990; 40:320-321
18. Mertz FP, Yao, RC. Streptosporangium carneum sp. nov. Isolated from soil. Int J Syst Bacteriol 1990; 40:247-253
19. Wink, JM. http://www.gbif-prokarya.de/-microorganisms/files/Methods.pdf. 2009
20. Wink JM. Compendium of Actinobacteria. http://www.dsmz.de/microorganisms/wink_pdf/DSM43021.pdf. 2009
21. Zhang LP, Zhang LM, Zhang XM. Streptosporangium canum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:1715-1719. PubMed doi:10.1099/ijs.0.007401-0
22. Biological Agents. Technical rules for biological agents www.baua.de TRBA 466
23. 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
24. Shearer MC, Colman PM, Nash CH, III. Streptosporangium fragile sp. nov. Int J Syst Bacteriol 1983; 33:364-368
25. Ochi K, Miyadoh S. Polyacrylamide Gel Electrophoresis Analysis of Ribosomal Protein AT-L30 from an Actinomycete Genus, Streptosporangium. Int J Syst Bacteriol 1992; 42:151-155. PubMed
26. Gyobu Y, Miyadoh S. Proposal to transfer Actinomadura carminata to a new subspecies of the genus Nonomuraea as Nonomuraea roseoviolacea subsp. carminata comb. nov. Int J Syst Evol Microbiol 2001; 51:881-889. PubMed
27. Kudo T, Seino A. Transfer of Streptosporangium indianense Gupta 1965 to the Genus Streptomyces as Streptomyces indiaensis (Gupta 1965) comb. nov. Int J Syst Bacteriol 1987; 37:241-244
28. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
29. 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 encyclopedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMeddoi:10.1038/nature08656
30. T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
31. Anonymous. http://compbio.ornl.gov/prodigal/
32. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A gene prediction improvement pipeline for mirobial genomes. (Submitted)
33. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. Expert review of functional annotations for microbial genomes. Bioinformatics 2009; 25:2271-2278. PubMeddoi:10.1093/bioinformatics/btp393