Complete genome sequence of Nakamurella multipartita type strain (Y-104 T)

Standards in Genomic Sciences

Volumn 2, Issue 2, 2010, Pages 168-175

  Tice, Hope ^a   Mayilraj, Shanmugam ^b,c   Sims, David ^d   Lapidus, Alla ^a   Nolan, Matt ^a   Lucas, Susan ^a   Glavina Del Rio, Tijana ^a   Copeland, Alex ^a   Cheng, Jan Fang ^a   Meincke, Linda ^d   Bruce, David ^a,d   Goodwin, Lynne ^a,d   Pitluck, Sam ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Ovchinnikova, Galina ^a   Pati, Amrita ^a   Chen, Amy ^e   Palaniappan, Krishna ^e   Land, Miriam ^a,f   Hauser, Loren ^a,f   Chang, Yun Juan ^a,f   Jeffries, Cynthia D ^a,f   Detter, John C ^a,d   Brettin, Thomas ^a,d   Rohde, Manfred ^g   Göker, Markus ^b   Bristow, Jim ^a   Eisen, Jonathan A ^a,h   Markowitz, Victor ^d   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^b   Chen, Feng ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^c INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

^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

(H 4); Frankineae; GEBA; Gram positive; Microsphaeraceae; MK 8; Nonmotile; Polysaccharide accumulating; Septa forming

Indexed keywords

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); FRANKINEAE; NAKAMURELLA; NAKAMURELLA MULTIPARTITA; NAKAMURELLACEAE; POSIBACTERIA;

EID: 80053456933     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.721316     Document Type: Article

References (24)

1. Yoshimi Y, Hiraishi A, Nakamura K. Isolation and characterization of Microsphaera multipartita gen. nov., sp. nov., a polysaccharide-accumulating Gram-positive bacterium from activated sludge. Int J Syst Bacteriol 1996; 46:519-525.doi:10.1099/00207713-46-2-519
2. Tao TS, Yue YY, Chen WX, Chen WF. Proposal of Nakamurella gen. nov. as a substitute for the bacterial genus Microsphaera Yoshimi et al. 1996 and Nakamurellaceae fam. nov. as a substitute for the illegitimate bacterial family Microsphaeraceae Rainey et al. 1997. Int J Syst Evol Microbiol 2004; 54:999-1000. PubMed doi:10.1099/ijs.0.02933-0
3. Léveillé JH. Organisation et disposition méthodique des especes qui composent le genre Erysiphé. Ann Sci Nat Bot Ser 1851; 15:109-179.
4. Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA, eds. International Code of Nomenclature of Bacteria (1990 revision). Bac-teriological Code. American Society for Microbiology, Washington DC, 1992.
5. 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. doi:10.1099/00207713-47-2-479
6. Rintala H, Pitkaranta M, Toivola M, Paulin L, Nevalainen A. Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 2008; 8:56.PubMed doi:10.1186/1471-2180-8-56
7. Yoon JH, Kang SJ, Jung SY, Oh TK. Humicoccus flavidus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:56-59 PubMed doi:10.1099/ijs.0.64246-0
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. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552 PubMed
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, 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
12. T). Stand Genomic Sci 2010; 2:158-167.
13. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, et al. Cenome characteristics of facultatively symbiontic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 2006; 17:7-15 PubMed doi:10.1101/gr.5798407
14. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen JA, Angiuoli 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
15. 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
16. 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, Springer, New York, 2001, p. 119-169.
17. Biological Agents. Classification of Bacteria and Archaea in risk groups. www.baua.de TRBA 466.
18. 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
19. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
20. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic en-cyclopedia of Bacteria and Archaea. Nature 2009; 462:1056-1060 PubMed doi:10.1038/nature08656
21. T). Stand Genomic Sci 2009; 1:12-20 doi:10.4056/sigs.761
22. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioin-formatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
23. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods (In press).
24. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278 PubMed doi:10.1093/bioinformatics/btp393