Complete genome sequence of Saccharomonospora viridis type strain (P101 T)

Standards in Genomic Sciences

Volumn 1, Issue 2, 2009, Pages 141-149

  Pati, Amrita ^a   Sikorski, Johannes ^b   Nolan, Matt ^a   Lapidus, Alla ^a   Copeland, Alex ^a   Glavina Del Rio, Tijana ^a   Lucas, Susan ^a   Chen, Feng ^a   Tice, Hope ^a   Pitluck, Sam ^a   Cheng, Jan Fang ^a   Chertkov, Olga ^a,c   Brettin, Thomas ^a,c   Han, Cliff ^a,c   Detter, John C ^a,c   Kuske, Cheryl ^a,c   Bruce, David ^a,c   Goodwin, Lynne ^a,c   Chain, Patrick ^a,d   D'haeseleer, Patrik ^a,d   Chen, Amy ^e   Palaniappan, Krishna ^e   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Rohde, Manfred ^f   Tindall, Brian J ^b   Göker, Markus ^b   Bristow, Jim ^a   Eisen, Jonathan A ^a,g   Markowitz, Victor ^d   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 LAWRENCE LIVERMORE 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

Bagassosis; Farmer's lung disease; Gram negative actinomycete; Hot compost; Humidifier fever; Pentachlorophenol metabolism; Pseudonocardiaceae; Thermophile

Indexed keywords

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); ARCHAEA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA; PSEUDONOCARDIACEAE; SACCHAROMONOSPORA; SACCHAROMONOSPORA VIRIDIS;

EID: 80053475268     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.20263     Document Type: Article

References (36)

1. Nonomura H, Ohara Y. Distribution of Actinomycetes in soil. (X) New genus and species of monosporic actinomycetes. J Ferment Technol 1971; 49:895-903.
2. Schuurmans DM, Olson BH, San Clemente CL. Production and isolation of thermoviridin, an antibiotic produced by Thermoactinomyces viridis n. sp. Appl Environ Microbiol 1956; 4:61-66.
3. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 1997; 47:590-592. PubMed
4. Amner W, Edwards C, McCarthy AJ. Improved medium for recovery and enumeration of the farmer's lung organism, Saccharomonospora viridis. Appl Environ Microbiol 1989; 55:2669-2674. PubMed
5. Roussel S, Reboux G, Dalphin JC, Pernet D, Laplante JJ, Millon L, Piarroux R. Farmer's Lung Disease and Microbiological Composition of Hay: A Case Control Study. Mycopathologia 2005; 160:273-279. PubMed doi:10.1007/s11046-0050155-6
6. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thompson N, Allen MJ, Angiuoli SV, et al. Towards a richer description of our complete collection of genomes and metagenomes: the "Minimum Information about a Genome Sequence" (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
7. 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
8. nd Ed. Vol 1 The Arc-haea, Deeply Branching and Phototrophic Bacteria. 2001 pp. 155-166
9. 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.
10. Wink JM. Compendium of Actinobacteria. http://www.gbif-prokarya.de/microorganisms/wink_pdf/DSM43017.pdf 2009.
11. Greiner-Mai E, Korn-Wendisch F, Kutzner HJ. Taxonomic revision of the genus Saccharomonospora and description of Saccharomonospora glauca sp. nov. Int J Syst Bacteriol 1988; 38:398-405.
12. Küster E, Locci R. Studies on peat and peat micro organisms. I. Taxonomic studies on thermophilic Actinomycetes isolated from peat. Arch Microbiol 1963; 45:188-197.
13. Steger K, Jarvis Å, Vasara T, Romantschuk M, Sundh I. Effects of differing temperature management on development of Actinobacteria populations during composting. Res Microbiol 2007; 158:617-624. PubMed doi:10.1016/j.resmic.2007.05.006
14. Webb MD, Ewbank G, Perkins J, McCarthy AJ. Metabolism of pentachlorophenol by Saccharomonospora viridis strains isolated from mushroom compost. Soil Biol Biochem 2001; 33:1903-1914. doi:10.1016/S0038-0717(01)00115-8
15. Anonymous. Biological Agents: Technical rules for biological agents www.baua.de TRBA 466.
16. 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
17. Dees PM. WCG. Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 2001; 35:207-216. PubMed doi:10.1111/j.1574-6941.2001.tb00805.x
18. Venter JC, Remington K, Heidelberg J, Halpern A, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304:66-74. PubMed doi:10.1126/science.1093857
19. 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
20. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
21. 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
22. 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
23. Fogarty WM, Collins BS, Doyle EM, Kelly CT. The high maltose-forming -amylase of Saccharomo-nospora viridis: mechanisms of action. J Ind Microbiol Biotechnol 1993; 11:199-204.
24. 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 (In press)
25. T). SIGS 2009; 1:12-20.
26. 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
27. 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
28. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted) 2009
29. 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
30. 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
31. 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
32. Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis 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
33. Karp PD, Paley SM, Romero P. The Pathway Tools Software. Bioinformatics 2002; 18:S225-S232.
34. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley SM, Rhee SY, Shearer A, Tissier B et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of pathway/Genome Databases. Nucleic Acids Res 2008; 36:D623-D631. PubMed
35. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky 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
36. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php