Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T)

Standards in Genomic Sciences

Volumn 4, Issue 1, 2011, Pages 36-44

  Gronow, Sabine ^a   Munk, Christine ^b,c   Lapidus, Alla ^b   Nolan, Matt ^b   Lucas, Susan ^b   Hammon, Nancy ^b   Deshpande, Shweta ^b   Cheng, Jan Fang ^b   Tapia, Roxane ^b,c   Han, Cliff ^b,c   Goodwin, Lynne ^b,c   Pitluck, Sam ^b   Liolios, Konstantinos ^b   Ivanova, Natalia ^b   Mavromatis, Konstantinos ^b   Mikhailova, Natalia ^b   Pati, Amrita ^b   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^b,e   Hauser, Loren ^b,e   Chang, Yun Juan ^b,e   Jeffries, Cynthia D ^b,e   Brambilla, Evelyne ^a   Rohde, Manfred ^f   Göker, Markus ^a   Detter, John C ^b,c   Woyke, Tanja ^b   Bristow, James ^b   Eisen, Jonathan A ^b,g   Markowitz, Victor ^d   Hugenholtz, Philip ^b,h   Kyrpides, Nikos C ^b   Klenk, Hans Peter ^a   more..

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

^b DOE JOINT GENOME INSTITUTE   (United States)

^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)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Anoxic rice field soil; Chemoorganotrophic; GEBA; Gram negative; Mesophilic; Nonmotile; Porphyromonadaceae; Strictly anaerobic

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); DYSGONOMONAS; NEGIBACTERIA; PALUDIBACTER; PALUDIBACTER PROPIONICIGENES; PORPHYROMONADACEAE;

EID: 80053379167     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1503846     Document Type: Article

References (30)

1. Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.
2. Ueki A, Akasaka H, Suzuki D, Ueki K. Paludibac-ter propionicigenes gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan. Int J Syst Evol Microbiol 2006; 56:39-44. PubMed doi:10.1099/ijs.0.63896-0
3. Akasaka H, Izawa T, Ueki K, Ueki A. Phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil. FEMS Micro-biol Ecol 2003; 43:149-161. PubMed doi:10.1111/j.1574-6941.2003.tb01054.x
4. Pei CX, Liu Q, Dong CS, Li H, Jiang JB, Gao WJ. Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas (Lama pacos) and sheep (Ovis aries). Anaerobe 2010; 16:426-432. PubMed doi:10.1016/j.anaerobe.2010.06.004
5. de Santis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Com-patible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi:10.1128/AEM.03006-05
6. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137.
7. 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
8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
9. 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
10. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How Many Bootstrap Replicates Are Necessary? Lect Notes Comput Sci 2009; 5541:184-200. doi:10.1007/978-3-642-02008-7_13
11. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes OnLine 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. Xu J, Mahowald MA, Ley RE, Lozupone CA, Ha-mady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 2007; 5:e156. PubMed doi:10.1371/journal.pbio.0050156
13. Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H, Nakayama K, Toh H, Yo-shimura F, Kuhara S, et al. Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rear-rangements in P. gingivalis. DNA Res 2008; 15:215-225. PubMed doi:10.1093/dnares/dsn013
14. 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
15. 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
16. Garrity GM, Holt JG. Taxonomic Outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Syste matic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 155-166.
17. Ludwig W, Euzeby J, Whitman WG. Draft tax-onomic outline of the Bacteroidetes, Planctomy-cetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf.
18. BAuA. Classification of bacteria and archaea in risk groups. TRBA 2005; 466:84.
19. 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
20. Klenk HP, Goeker 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
21. 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
22. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
23. DOE Joint Genome Institute. http://www.jgi.doe.gov
24. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
25. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed doi:10.1101/gr.074492.107 26
26. Han C, Chain P. 2006. Finishing repeat regions automatically with Dupfinisher. in Proceeding of the 2006 international conference on bioinfor-matics & computational biology. Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26- 29, 2006: 141-146
27. 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.
28. Hyatt D, Chen GL, LoCascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
29. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
30. 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