Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801T)

Standards in Genomic Sciences

Volumn 7, Issue 1, 2012, Pages 120-130

  Riedel, Thomas ^a   Held, Brittany ^b,c   Nolan, Matt ^b   Lucas, Susan ^b   Lapidus, Alla ^b   Tice, Hope ^b   Del Rio, Tijana Glavina ^b   Cheng, Jan Fang ^b   Han, Cliff ^b,c   Tapia, Roxanne ^b,c   Goodwin, Lynne A ^b,c   Pitluck, Sam ^b   Liolios, Konstantinos ^b   Mavromatis, Konstantinos ^b   Pagani, Ioanna ^b   Ivanova, Natalia ^b   Mikhailova, Natalia ^b   Pati, Amrita ^b   Chen, Amy ^d   Palaniappan, Krishna ^d   Rohde, Manfred ^a   Tindall, Brian J ^f   Detter, John C ^b,c   Göker, Markus ^f   Woyke, Tanja ^b   Bristow, James ^b   Eisen, Jonathan A ^b,g   Markowitz, Victor ^d   Hugenholtz, Philip ^b,h   Klenk, Hans Peter ^f   Kyrpides, Nikos C ^b,e   more..

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (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 LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Aerobic; Bacteroidetes; Cryomorphaceae; Flavobacteria; GEBA; Gram negative; Mesophilic; Motile; Non fermentative; Orange pigmented sea water; Rod shaped

Indexed keywords

BACTERIAL DNA; BETA CAROTENE; FATTY ACID; RNA 16S; SEA WATER;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CLASSIFICATION; DNA ISOLATION; GENE SEQUENCE; MARINE BACTERIUM; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORANGE PIGMENTATION; OWENWEEKSIA HONGKONGENSIS; PHYLOGENETIC TREE; PIGMENTATION; TAXONOMY;

BACTERIA (MICROORGANISMS); BACTEROIDETES; CRYOMORPHACEAE; FLAVOBACTERIA; NEGIBACTERIA; OWENWEEKSIA; OWENWEEKSIA HONGKONGENSIS;

EID: 84868299124     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3296896     Document Type: Article

References (52)

1. Lau KWK, Ng CYM, Ren J, Lau SCL, Qian PY, Wong PK, Lau TC, Wu M. Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes'. Int J Syst Evol Microbiol 2005; 55:1051-1057. PubMed http://dx.doi.org/10.1099/ijs.0.63155-0
2. Delong EF, Franks DG, Alldredge AL. Phylogenet-ic diversity of aggregate-attached versus free-living marine bacterial assemblages. Limnol Oceanogr 1993; 38:924-934. http://dx.doi.org/10.4319/lo.1993.38.5.0924
3. Rath J, Wu KY, Herndl GJ, DeLong EF. High phy-logenetic diversity in a marine-snow-associated bacterial assemblage. Aquat Microb Ecol 1998; 14:261-269. http://dx.doi.org/10.3354/ame014261
4. Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, Marrasé C. Changes in bacterioplancton composition under different phytoplankton regimes. Appl Environ Microbiol 2004; 70:6753-6766. PubMed http://dx.doi.org/10.1128/AEM.70.11.6753-6766.2004
5. Riemann L, Steward GF, Azam F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol 2000; 66:578-587. PubMed http://dx.doi.org/10.1128/AEM.66.2.578-587.2000
6. Cottrell MT, Kirchman DL. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low-and high-molecular weight dissolved organic matter. Appl Environ Microbiol 2000; 66:1692-1697. PubMed http://dx.doi.org/10.1128/AEM.66.4.1692-1697.2000
7. Kirchman DL. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 2002; 39:91-100. PubMed
8. Anderson KL, Salyers AA. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch binding sites and periplasmatic starch-degrading enzymes. J Bacteriol 1989; 171:3192-3198. Pub-Med
9. Anderson KL, Salyers AA. Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 1989; 171:3199-3204. PubMed
10. Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Würdemann CA, Quast C, Kuhl H, Knaust F, et al. Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' re-veals adaption to degradation of polymeric organ-ic matter. Environ Microbiol 2006; 8:2201-2213. PubMed http://dx.doi.org/10.1111/j.1462-2920.2006.01152.x
11. González JM, Fernández-Gómez B, Fernàndez-Guerra A, Gómez-Consarnau L, Sánchez O, Coll-Lladó M, Del Campo J, Escudero L, Rodriguez-Martinez R, Alsonso-Sáez L, et al. Genome analy-sis of the proteorhodopsin-containing marine bac-terium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci USA 2008; 105:8724-8729. PubMed http://dx.doi.org/10.1073/pnas.0712027105
12. Bowman JP, Mancuso Nichols C, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., nov-el flavobacteria isolated from various polar habi-tats. Int J Syst Evol Microbiol 2003; 53:1343-1355. PubMed http://dx.doi.org/10.1099/ijs.0.02553-0
13. Lau KW, Ren J, Wai NL, Qian PY, Wong PK, Wu M. Lishizhenia caseinilytica gen. nov., sp. nov., a marine bacterium of the phylum Bacteroidetes. Int J Syst Evol Microbiol 2006; 56:2317-2322. PubMed http://dx.doi.org/10.1099/ijs.0.64415-0
14. Lee DH, Choi EK, Moon SR, Ahn S, Lee YS, Jung JS, Jeon CO, Whang KS, Kahng HY. Wandonia haliotis gen. nov., sp. nov., a marine bacterium of the family Cryomorphaceae, phylum Bacteroidetes. Int J Syst Evol Microbiol 2010; 60:510-514. PubMed http://dx.doi.org/10.1099/ijs.0.012674-0
15. Zhou Y, Su J, Lai Q, Li X, Yang X, Dong P, Zheng T. Phaeocystidibacter luteus gen. nov. sp. nov., a new member of the family Cryomorphaceae iso-lated from the marine alga Phaeocystis globosa and emended description of Owenweeksia hongkongensis. Int J Syst Evol Microbiol 2012. PubMed http://dx.doi.org/10.1099/ijs.0.030254-0
16. O'Sullivan LA, Rinna J, Humphreys G, Weightman AJ, Fry JC. Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the Phylum 'Bacteroidetes'. Int J Syst Evol Microbiol 2005; 55:2189-2194. PubMed http://dx.doi.org/10.1099/ijs.0.63736-0
17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
18. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Se-bastopol, 2003.
19. DeSantis 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 compat-ible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed http://dx.doi.org/10.1128/AEM.03006-05
20. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137.
21. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
22. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. Pub-Med http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
23. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
24. 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
25. 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. http://dx.doi.org/10.1007/978-3-642-02008-7_13
26. Swofford DL. PAUP*: Phylogenetic Analysis Us-ing Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
27. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their as-sociated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed http://dx.doi.org/10.1093/nar/gkr1100
28. T). Stand Genomic Sci 2011; 5:21-29. PubMed http://dx.doi.org/10.4056/sigs.2124912
29. 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 genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
30. Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
31. 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 http://dx.doi.org/10.1073/pnas.87.12.4576
32. Krieg NR, Ludwig W, Euzéby J, Whitman WB. Phylum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 25.
33. Validation List No. 143. [PubMed]. Int J Syst Evol Microbiol 2012; 62:1-4.
34. Bernardet JF. Class II. Flavobacteria class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Pas-ter BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Se-cond Edition, Volume 4, Springer, New York, 2011, p. 105.
35. Ludwig W, Euzeby J, Whitman WG. Draft taxo-nomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes.
36. Judicial Commission of the International Commit-tee on Systematics of Prokaryotes. The nomencla-tural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005.
37. Bernardet JF. Order I. Flavobacteriales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 4, Springer, New York, 2011, p. 105.
38. Errata: List of new names and new combinations previously effectively, but not validly, published-Validation List No. 143. Int J Syst Evol Microbiol 2012; 62:1016. http://dx.doi.org/10.1099/ijs.0.68147-0
39. BAuA. 2010, Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 466, p. 158.
40. 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. The Gene Ontology Con-sortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
41. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/10.1016/j.syapm.2010.03.003
42. 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 http://dx.doi.org/10.1038/nature08656
43. List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/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 German 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 novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
48. Han C, Chain P. Finishing repeat regions auto-matically with Dupfinisher. In: Proceedings of the 2006 international conference on bioinformatics & computational 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 us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
50. Hyatt D, Chen GL, Locascio PF, Land ML, Lar-imer FW, Hauser LJ. Prodigal Prokaryotic Dynam-ic Programming Genefinding Algorithm. BMC Bi-oinformatics 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 mi-crobial genomes. Nat Methods 2010; 7:455-457. PubMed 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. Bio-informatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393