Complete genome sequence of Thermobispora bispora type strain (R51 T)

Standards in Genomic Sciences

Volumn 2, Issue 3, 2010, Pages 318-326

  Liolios, Konstantinos ^a   Sikorski, Johannes ^b   Jando, Marlen ^b   Lapidus, Alla ^a   Copeland, Alex ^a   del Rio, Tijana Glavina ^a   Nolan, Matt ^a   Lucas, Susan ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Han, Cliff ^a,c   Woyke, Tanja ^a   Goodwin, Lynne ^a,c   Pitluck, Sam ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Chertkov, Olga ^a   Kuske, Cheryl ^a   Chen, Amy ^d   Palaniappan, Krishna ^a,e   Land, Miriam ^a,e   Hauser, Loren ^a,e   Chang, Yun Juan ^a,e   Jeffries, Cynthia D ^a,e   Detter, John C ^a,e   Brettin, Thomas ^a,e   Rohde, Manfred ^a   Göker, Markus ^f   Bristow, James ^b   Eisen, Jonathan A ^a   Markowitz, Victor ^a,g   Hugenholtz, Philip ^d   Klenk, Hans Peter ^a   Kyrpides, Nikos C ^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 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)

Author keywords

GEBA; Non pathogenic; Streptospo rangineae; Strictly thermophilic; Two distinct 16s rRNA genes

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); THERMOBISPORA; THERMOBISPORA BISPORA;

EID: 80053373898     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.962171     Document Type: Article

References (33)

1. Wang Y, Zhang Z, Ruan J. A proposal to transfer Microbispora bispora (Lechevalier 1965) to a new genus, Thermobispora gen. nov., as Thermobispo-ra bispora comb. nov. Int J Syst Bacteriol 1996; 46:933-938. PubMed doi:10.1099/00207713-46-4-933
2. Henssen A. Beiträge zur Morphologie und Syste-matik der thermophilen Actinomyceten. Arch Mi-crobiol 1957; 26:373-414. doi:10.1007/BF00407588
3. Steger K, Jarvis A, Vasara T, Romantschuk M, Sundh I. Effects of differing temperature manage- ment on development of Actinobacteria popula-tions during composting. Res Microbiol 2007; 158:617-624 PubMed doi:10.1016/j.resmic.2007.05.006
4. Nonomura H, Ohara I. On a new actinomycete, Microbispora, isolated from soil. Abstract 98, pages 31 and 32, Abstracts of papers presented at the annual meeting of the Agricultural Chemical Society of Japan. Tokyo University, April 9th to llth, 1957. Published by the Agricultural Chemi-cal Society (in Japanese). 1957.
5. Henssen A, Schnepf E. Zur Kenntnis thermophiler Actinomyceten. Arch Microbiol 1967; 57:214-231. doi:10.1007/BF00405948
6. Lechevalier HA. Priority of the generic name Mi-crobispora over Waksmania and Thermopolyspo-ra. Int Bull Bacteriol Nomencl Taxon 1965; 15:139-142. doi:10.1099/00207713-15-3-139
7. Miyadoh S, Amano S, Tohyama H, Shomura T. A taxonomic review of the genus Microbispora and a proposal to transfer two species to the genus Ac-tinomadura and to combine ten species into Mi-crobispora rosea. J Gen Microbiol 1990; 136:1905-1913. PubMed
8. Ochi K, Haraguchi K, Miyadoh S. A taxonomic review of the genus Microbispora by analysis of ribosomal protein AT-L30. Int J Syst Bacteriol 1993; 43:58-62. PubMed doi:10.1099/00207713-43-1-58
9. Wang Y, Zhang Z, Ramanan N. The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 1997; 179:3270-3276. PubMed
10. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the iden-tification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259-2261. PubMed doi:10.1099/ijs.0.64915-0
11. Thawai C, Tanasupawat S, Kudo T. Micromonos-pora pattaloongensis sp. nov., isolated from Thai mangrove forest. Int J Syst Evol Microbiol 2008; 58:1516-1521. PubMed doi:10.1099/ijs.0.65410-0
12. Tamura T, Sakane T. Planotetraspora silvatica sp. nov.,and emended description of the genus Pla-notetraspora. Int J Syst Evol Microbiol 2004; 54:2053-2056. PubMed doi:10.1099/ijs.0.02981-0
13. 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.
14. Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based de-finition of higher ranks of the class Actinobacte-ria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589-608. PubMed doi:10.1099/ijs.0.65780-0
15. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
16. 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
17. 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
18. Yarza P, Richter M, Peplies J, Euzeby JP, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rossel-lo-Mora R. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all se-quenced type strains. Syst Appl Microbiol 2008; 31:241-250. PubMed doi:10.1016/j.syapm.2008.07.001
19. 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 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
20. Nolan M, Sikorski J, Jando M, Lucas S, Lapidus A, Glavina Del Rio T, Chen F, Tice H, Pitlick S, Cheng JF, et al. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T). Stand Genomic Sci 2010; 2:29-37. doi:10.4056/sigs.631049
21. Allgaier M, Reddy A, Park JI, Ivanova N, D'haese-leer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS et al. Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS ONE 2010; 5:e8812. PubMed doi:10.1371/journal.pone.0008812
22. 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
23. 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
24. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification sys-tem, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479-491. doi:10.1099/00207713-47-2-479
25. Classification of bacteria and archaea in risk groups. http://www.baua.deTRBA466.
26. 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. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
27. 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
28. 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 sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
29. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
30. Sims D, Brettin T, Detter J, Han C, Lapidus A, Co-peland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Ky-tococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
31. Hyatt D, Chen GL, LoCascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. 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. GenePRIMP: A gene prediction improvement ipeline for mi-crobial 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 ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393