Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207 T)

Standards in Genomic Sciences

Volumn 3, Issue 1, 2010, Pages 85-92

  Labutti, kurt ^a   Mayilraj, Shanmugam ^b,g   Clum, Alicia ^a   Lucas, Susan ^a   del Rio, Tijana Glavina ^a   Nolan, Matt ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Pati, Amrita ^a   Goodwin, Lynne ^a,c   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^a,e   Hauser, Loren ^a,e   Chang, Yun Juan ^a,e   Jeffries, Cynthia D ^a,e   Rohde, Manfred ^f   Spring, Stefan ^g   Göker, Markus ^g   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,h   Markowitz, Victor ^d   Hugenholtz, Philip ^a   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^g   Lapidus, Alla ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

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

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Anaerobic; GEBA; H 2S producing; Motile; Peptide uti lization; Synergistaceae; Synergistetes; Thiosulfate reducing; Vibrio shaped

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); DETHIOSULFOVIBRIO PEPTIDOVORANS; THERMOANAEROBACTER; VIBRIO;

EID: 80053341988     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1092865     Document Type: Article

References (23)

1. Magot M, Ravot G, Campaignolle X, Ollivier B, Patel BKC, Fardeau ML, Thomas P, Crolet JL, Garcia JL. Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophil-ic, thiosulfate-reducing bacterium from corroding offshore oil wells. [9226912]. Int J Syst Bacteriol 1997; 47:818-824; doi:10.1099/00207713-47-3-818. PubMed
2. Jumas-Bilak E, Roudière L, Marchandin H. De-scription of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomo-nadaceae, phylum 'Firmicutes'. [19406787]. Int J Syst Evol Microbiol 2009; 59:1028-1035. doi:10.1099/ijs.0.006718-0. PubMed
3. Diaz-Cárdenas C, López G, Patel BKC, Baena S. Dethiosukfovibrio salsuginis sp. nov., an anaerob-ic slightly halophilic bacterium isolated from a sa-line spring in Colombia. Int J Syst Bacteriol 2009, (In press); 10.1099/ijs.0.010835-0.
4. Surkov AV, Dubinina GA, Lysenko AM, Glöckner FO, Kuever J. Dethiosulfovibrio russensis sp. nov., Dethiosulfovibrio marinus sp. nov. and Dethiosul-fovibrio acidaminovorans sp. nov., novel anae-robic, thiosulfate-and sulfur-reducing bacteria isolated from 'Thiodendron' sulfur mats in differ-ent saline environments. Int J Syst Evol Microbiol 2001; 51:327-337. PubMed
5. 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
6. 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
7. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
8. 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
9. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra 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
10. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes OnLine Database (GOLD) in 2009: status of genomic and metage-nomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
11. Chovatia M, Sikorski J, Schöder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF, Lucas S, et al. Complete genome se-quence of Thermanaerovibrio acidaminovorans type strain (Su883T). Stand Genomic Sci 2009; 1:254-261. doi:10.4056/sigs.40645
12. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, et al. Complete genome se-quence of Aminobacterium colombiense type strain (ALA-1T). Stand Genomic Sci 2010; 2:280-289. doi:10.4056/sigs.902116
13. 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
14. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms. Proposal for the do-mains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
15. Classification of bacteria and archaea in risk groups. www.baua.de TRBA 466
16. 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 un-ification of biology. The Gene Ontology Consor-tium. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
17. 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
18. 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 encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed doi:10.1038/nature08656.
19. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
20. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
21. Hyatt D, Chen GL, Locascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal Prokaryotic Dynam-ic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
22. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A gene prediction improvement pipeline for mi-crobial genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
23. 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