Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)

Standards in Genomic Sciences

Volumn 6, Issue 2, 2012, Pages 220-229

  Klenk, Hans Peter ^a   Held, Brittany ^b   Lucas, Susan ^c   Lapidus, Alla ^c   Copeland, Alex ^c   Hammon, Nancy ^c   Pitluck, Sam ^c   Goodwin, Lynne A ^b,c   Han, Cliff ^b,c   Tapia, Roxanne ^b,c   Brambilla, Evelyne Marie ^a   Pötter, Gabriele ^a   Land, Miriam ^c,d   Ivanova, Natalia ^c   Rohde, Manfred ^e   Göker, Markus ^a   Detter, John C ^b,c   Kyrpides, Nikos C ^c   Woyke, Tanja ^c  

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

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

Aerobic; Chemoheterotrophic; CSP 2010; Gram positive; Non motile; Pseudonocardiaceae; Soil bacterium; Spore forming; Vegetative and aerial mycelia

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; CHEMOTAXONOMY; DNA ISOLATION; GENE SEQUENCE; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; RNA SEQUENCE; SACCHAROMONOSPORA AZUREA; SOIL MICROFLORA;

BACTERIA (MICROORGANISMS); POSIBACTERIA; PSEUDONOCARDIACEAE; SACCHAROMONOSPORA; SACCHAROMONOSPORA AZUREA; SACCHAROMONOSPORA VIRIDIS;

EID: 84863600946     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2635833     Document Type: Article

References (52)

1. Runmao H. Saccharomonospora azurea sp. nov., a new species from soil. Int J Syst Bacteriol 1987; 37:60-61. http://dx.doi.org/10.1099/00207713-37-1-60
2. Garrity G. NamesforLife. BrowserTool takes exper-tise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
3. Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the internet. Int J Syst Bacteriol 1997; 47:590. PubMed http://dx.doi.org/10.1099/00207713-47-2-590
4. Yoon JH, Kim SB, Lee ST, Park YH. DNA-DNA re-latedness between Saccharomonospora species: 'Saccharomonospora caesia' as a synonym of Saccharomonospora azurea. Int J Syst Bacteriol 1999; 49:671-673. http://dx.doi.org/10.1099/00207713-49-2-671
5. Kurup VP. Taxonomic study of some members of Micropolyspora and Saccharomonospora. Microbiologica 1981; 4:249-259.
6. Kalakoutskii LV. A new species of the genus Micropolyspora-Micropolyspora caesia n. sp. [Eng-lish translation of Microbiologiya]. Microbiology 1964; 33:765-768.
7. Skerman VBD, McGowan V, Sneath PHA. Ap-proved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
8. T). Stand Genomic Sci 2009; 1:141-149. PubMed http://dx.doi.org/10.4056/sigs.20263
9. 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 En-cyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed http://dx.doi.org/10.1038/nature08656
10. Carbon Active Enzyme Database. http://www.cazy.org
11. Liu Z, Li Y, Zheng L, Huang YJ, Li WJ. Saccharomonospora marina sp. nov., isolated from an ocean sediment of the East China Sea. Int J Syst Evol Microbiol 2010; 60:1854-1857. PubMed http://dx.doi.org/10.1099/ijs.0.017038-0
12. Al-Zarban SS, Al-Musaallam AA, Abbas I, Stackebrandt E, Kroppenstedt RM. Saccharomonospora halophila sp. nov., a novel halophilic actinomycete isolated from marsh soil in Kuwait. Int J Syst Evol Microbiol 2002; 52:555-558. PubMed
13. Syed DG, Tang SK, Cai M, Zhi XY, Agasar D, Lee JC, Kim CJ, Jiang CL, Xu CL, Li WJ. Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil. Int J Syst Evol Microbiol 2008; 58:570-573. PubMed http://dx.doi.org/10.1099/ijs.0.65449-0
14. Li WJ, Tang SK, Stackebrandt E, Kroppenstedt RM, Schumann P, Xu LH, Jiang CL. Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China. Int J Syst Evol Microbiol 2003; 53:1591-1594. PubMed http://dx.doi.org/10.1099/ijs.0.02633-0
15. Jin X, Xu LH, Mao PH, Hseu TH, Jiang CL. Descrip-tion of Saccharomonospora xinjiangensis sp. nov. based on chemical and molecular classification. Int J Syst Bacteriol 1998; 48:1095-1099. PubMed http://dx.doi.org/10.1099/00207713-48-4-1095
16. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
17. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebas-topol, 2003.
18. DeSantis 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 http://dx.doi.org/10.1128/AEM.03006-05
19. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137.
20. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
21. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
22. Stamatakis A, Hoover P, Rougemont J. A rapid boot-strap algorithm for the RAxML web servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
23. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
24. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap rep-licates are necessary? Lect Notes Comput Sci 2009; 5541:184-200. http://dx.doi.org/10.1007/978-3-642-02008-7_13
25. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
26. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Kyrpides NC. The genomes on line database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metada-ta. Nucleic Acids Res 2010; 38:D346-D354. Pub-Med http://dx.doi.org/10.1093/nar/gkp848
27. T). Stand Genomic Sci 2009; 1:46-53. PubMed http://dx.doi.org/10.4056/sigs.21137
28. T). Stand Genomic Sci 2010; 2:318-326. PubMed http://dx.doi.org/10.4056/sigs.962171
29. Tang SK, Wang Y, Klenk HP, Shi R, Lou K, Zhang YJ, Chen C, Ruan JS, Li WJ. Actinopolyspora alba sp. nov. and Actinopolyspora erythraea sp. nov., isolat-ed from a salt field, and reclassification of Actinopolyspora iraqiensis Ruan et al. 1994 as a heterotypic synonym of Saccharomonospora halophila. Int J Syst Evol Microbiol 2011; 61:1693-1698. PubMed http://dx.doi.org/10.1099/ijs.0.022319-0
30. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a ge-nome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
31. Woese CR, Kandler O, Wheelis ML. Towards a nat-ural system of organisms. Proposal for the domains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
32. 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.
33. Stackebrandt E, Rainey FA, Ward-Rainey NL. Pro-posal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479-491. http://dx.doi.org/10.1099/00207713-47-2-479
34. Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based defi-nition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the exist-ing higher taxa. Int J Syst Evol Microbiol 2009; 59:589-608. PubMed http://dx.doi.org/10.1099/ijs.0.65780-0
35. Buchanan RE. Studies in the nomenclature and clas-sification of bacteria. II. The primary subdivisions of the Schizomycetes. J Bacteriol 1917; 2:155-164. PubMed
36. Labeda DP, Goodfellow M, Chun J, Zhi X-Y, Li W-J. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2011; 61:1259-1264. PubMed http://dx.doi.org/10.1099/ijs.0.024984-0
37. List Editor. Validation List no. 29. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1989; 39:205-206. http://dx.doi.org/10.1099/00207713-39-2-205
38. Embley MT, Smida J, Stackebrandt E. The phylogeny of mycolate-less wall chemotype IV Actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 1988; 11:44-52. http://dx.doi.org/10.1016/S0723-2020(88)80047-X
39. Nonomura H, Ohara Y. Distribution of actinomycetes in soil. X. New genus and species of monosporic actinomycetes in soil. J Ferment Technol 1971; 49:895-903.
40. BAuA. 2010, Classification of Bacteria and Archaea in risk groups. http://www.baua.de TRBA 466, p. 194.
41. 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. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
42. Wink JM. Compendium of Actinobacteria. http://www.dsmz.de/microorganisms/wink_pdf/DSM44631.pdf.
43. List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technolog y/list-of-media-for-microorganisms.html.
44. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a Ger-man initiative. Biopreserv Biobank 2011; 9:51-55. http://dx.doi.org/10.1089/bio.2010.0029
45. The DOE Joint Genome Institute. http://www.jgi.doe.gov
46. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
47. Zerbino DR, Birney E. Velvet: algorithms for de no-vo short read assembly using de Bruijn graphs. Ge-nome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
48. Han C, Chain P. Finishing repeat regions automati-cally with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & com-putational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26-29, 2006: 141-146.
49. 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.
50. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Pro-gramming Genefinding Algorithm. BMC Bioinfor-matics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
51. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbi-al genomes. Nat Methods 2010; 7:455-457. Pub-Med http://dx.doi.org/10.1038/nmeth.1457
52. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bioin-formatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393