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Volumn 6, Issue 1, 2012, Pages 74-83

Complete genome sequence of polynucleobacter necessarius subsp. Asymbioticus type strain (QLW-P1DMWA-1 T)

(29)  Meincke, Linda a,b   Copeland, Alex a   Lapidus, Alla a   Lucas, Susan a   Berry, Kerrie W a   del Rio, Tijana Glavina a   Hammon, Nancy a   Dalin, Eileen a   Tice, Hope a   Pitluck, Sam a   Richardson, Paul a   Bruce, David a,b   Goodwin, Lynne a,b   Han, Cliff a,b   Tapia, Roxanne a,b   Detter, John C a,b   Schmutz, Jeremy b   Brettin, Thomas a,c   Larimer, Frank a,c   Land, Miriam a,c   more..


Author keywords

Aerobic; Betaproteobacteria; Burkholderiaceae; Chemoorganotrophic; CSP2006; Free living; Freshwater habitats; Gram negative; Non motile; Planktonic

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; FRESH WATER;

EID: 84858697506     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2395367     Document Type: Article
Times cited : (27)

References (47)
  • 1
    • 70349329727 scopus 로고    scopus 로고
    • Emended description of the genus Polynucleobacter and the species Polynucleobacter necessarius and proposal of two subspecies, P
    • necessarius subsp. necessarius subsp. nov. and P. necessarius subsp. asymbioticus subsp. nov, PubMed
    • Hahn MW, Lang E, Brandt U, Wu QL, Scheuerl T. Emended description of the genus Polynucleobacter and the species Polynucleobacter necessarius and proposal of two subspecies, P. necessarius subsp. necessarius subsp. nov. and P. necessarius subsp. asymbioticus subsp. nov. Int J Syst Evol Microbiol 2009; 59:2002-2009. PubMed http://dx.doi.org/10.1099/ijs.0.005801-0
    • (2009) Int J Syst Evol Microbiol , vol.59 , pp. 2002-2009
    • Hahn, M.W.1    Lang, E.2    Brandt, U.3    Wu, Q.L.4    Scheuerl, T.5
  • 2
    • 0000495106 scopus 로고
    • Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus
    • Heckmann K, Schmidt HJ. Polynucleobacter necessarius gen. nov., sp. nov., an obligately endosymbiotic bacterium living in the cytoplasm of Euplotes aediculatus. Int J Syst Bacteriol 1987; 37:456-457. http://dx.doi.org/10.1099/00207713-37-4-456
    • (1987) Int J Syst Bacteriol , vol.37 , pp. 456-457
    • Heckmann, K.1    Schmidt, H.J.2
  • 3
    • 77951341820 scopus 로고
    • Symbiontes bactérienes des ciliés du genre Euplotes
    • In French
    • Fauré-Fremiet E. Symbiontes bactérienes des ciliés du genre Euplotes. [In French]. CR Acad Sci 1952; 235:402-403.
    • (1952) CR Acad Sci , vol.235 , pp. 402-403
    • Fauré-Fremiet, E.1
  • 4
    • 0141816854 scopus 로고    scopus 로고
    • Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats in three climatic zones
    • PubMed
    • Hahn MW. Isolation of strains belonging to the cosmopolitan Polynucleobacter necessarius cluster from freshwater habitats in three climatic zones. Appl Environ Microbiol 2003; 69:5248-5254. PubMed http://dx.doi.org/10.1128/AEM.69.9.5248-5254.2003
    • (2003) Appl Environ Microbiol , vol.69 , pp. 5248-5254
    • Hahn, M.W.1
  • 6
    • 77953917650 scopus 로고    scopus 로고
    • Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogeneous 2000 km2 area
    • PubMed
    • Jezberová J, Jezbera J, Brandt U, Lindström ES, Langenheder S, Hahn MW. Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogeneous 2000 km2 area. Environ Microbiol 2010; 12:658-669. PubMed http://dx.doi.org/10.1111/j.1462-2920.2009.02106.x
    • (2010) Environ Microbiol , vol.12 , pp. 658-669
    • Jezberová, J.1    Jezbera, J.2    Brandt, U.3    Lindström, E.S.4    Langenheder, S.5    Hahn, M.W.6
  • 7
    • 76849114725 scopus 로고    scopus 로고
    • Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers
    • PubMed
    • Hahn MW, Lang E, Brandt U, Lünsdorf H, Wu QL, Stackebrandt E. Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers. Int J Syst Evol Microbiol 2010; 60:166-173. PubMed http://dx.doi.org/10.1099/ijs.0.010595-0
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 166-173
    • Hahn, M.W.1    Lang, E.2    Brandt, U.3    Lünsdorf, H.4    Wu, Q.L.5    Stackebrandt, E.6
  • 8
    • 79952431875 scopus 로고    scopus 로고
    • Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake
    • PubMed
    • Hahn MW, Lang E, Tarao M, Brandt U. Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake. Int J Syst Evol Microbiol 2011; 61:781-787. PubMed http://dx.doi.org/10.1099/ijs.0.017350-0
    • (2011) Int J Syst Evol Microbiol , vol.61 , pp. 781-787
    • Hahn, M.W.1    Lang, E.2    Tarao, M.3    Brandt, U.4
  • 9
    • 79952368533 scopus 로고    scopus 로고
    • Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria
    • PubMed
    • Hahn MW, Lang E, Brandt U, Spröer C. Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria. Int J Syst Evol Microbiol 2011; 61:788-794. PubMed http://dx.doi.org/10.1099/ijs.0.023929-0
    • (2011) Int J Syst Evol Microbiol , vol.61 , pp. 788-794
    • Hahn, M.W.1    Lang, E.2    Brandt, U.3    Spröer, C.4
  • 10
    • 84855196459 scopus 로고    scopus 로고
    • Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter
    • In press, PubMed
    • Hahn MW, Minasyan A, Lang E, Koll U, Spröer C. Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. Int J Syst Evol Microbiol (In press). PubMed
    • Int J Syst Evol Microbiol
    • Hahn, M.W.1    Minasyan, A.2    Lang, E.3    Koll, U.4    Spröer, C.5
  • 11
    • 23744486525 scopus 로고    scopus 로고
    • Low intraspecific diversity in a Polynucleobacter subcluster popula-tion numerically dominating bacterioplankton of a freshwater pond
    • PubMed
    • Hahn MW, Pöckl M, Wu Q. L. Low intraspecific diversity in a Polynucleobacter subcluster popula-tion numerically dominating bacterioplankton of a freshwater pond. Appl Environ Microbiol 2005; 71:4539-4547. PubMed http://dx.doi.org/10.1128/AEM.71.8.4539-4547.2005
    • (2005) Appl Environ Microbiol , vol.71 , pp. 4539-4547
    • Hahn, M.W.1    Pöckl, M.2    Wu, Q.L.3
  • 12
    • 84858640813 scopus 로고    scopus 로고
    • The passive yet successful way of planktonic life: Genomic and experimental analysis of the ecology of a planctonic Polynucleobacter population
    • In press
    • Hahn MW, Scheuerl T, Jezberova J, Koll U, Jezbera J, Simek K, Vannini C, Petroni G, Wu QL. The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a planctonic Polynucleobacter population. PLoS ONE (In press).
    • PLoS ONE
    • Hahn, M.W.1    Scheuerl, T.2    Jezberova, J.3    Koll, U.4    Jezbera, J.5    Simek, K.6    Vannini, C.7    Petroni, G.8    Wu, Q.L.9
  • 16
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • PubMed
    • 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
    • (2002) Bioinformatics , vol.18 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 17
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Pub-Med
    • Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. Pub-Med
    • (2000) Mol Biol Evol , vol.17 , pp. 540-552
    • Castresana, J.1
  • 18
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • PubMed
    • 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
    • (2008) Syst Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 19
    • 36849014457 scopus 로고    scopus 로고
    • An empirical test of the midpoint rooting method
    • 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
    • (2007) Biol J Linn Soc Lond , vol.92 , pp. 669-674
    • Hess, P.N.1    de Moraes, R.C.A.2
  • 22
    • 75549086416 scopus 로고    scopus 로고
    • The genomes On line database (GOLD) in 2009: Status of genomic and metagenomic projects and their associated metadata
    • PubMed
    • 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 metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed http://dx.doi.org/10.1093/nar/gkp848
    • (2010) Nucleic Acids Res , vol.38
    • Liolios, K.1    Chen, I.M.2    Mavromatis, K.3    Tavernarakis, N.4    Kyrpides, N.C.5
  • 24
    • 77955908592 scopus 로고    scopus 로고
    • BrowserTool takes expertise out of the database and puts it right in the browser
    • NamesforLife
    • Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
    • (2010) Microbiol Today , vol.37 , pp. 9
    • Garrity, G.1
  • 25
    • 0025300402 scopus 로고
    • Towards a natural system of organisms
    • Proposal for the do-mains Archaea and Bacteria, PubMed
    • 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
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 26
    • 33646193540 scopus 로고    scopus 로고
    • Proteobacteria phyl
    • nov, Brenner DJ, Krieg NR, Staley JT, Garrity GM, second edition, The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York
    • Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 1.
    • (2005) Bergey's Manual of Systematic Bacteriology , vol.2 , pp. 1
    • Garrity, G.M.1    Bell, J.A.2    Lilburn, T.3    Phylum, X.I.V.4
  • 27
    • 33747880275 scopus 로고    scopus 로고
    • Betaproteobacteria class
    • nov, Garrity GM, Brenner DJ, Krieg NR, Staley JT, Second Edition, Part C, Springer, New York
    • Garrity GM, Bell JA, Lilburn T. Class II. Betaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.
    • (2005) Bergey's Manual of Systematic Bacteriology , vol.2 , pp. 575
    • Garrity, G.M.1    Bell, J.A.2    Lilburn, T.3    Class, I.I.4
  • 28
    • 33644852672 scopus 로고    scopus 로고
    • Validation List No. 107. List of new names and new combinations previously effectively, but not validly
    • published, PubMed
    • Editor L. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1-6. PubMed http://dx.doi.org/10.1099/ijs.0.64188-0
    • (2006) Int J Syst Evol Microbiol , vol.56 , pp. 1-6
    • Editor, L.1
  • 29
    • 33747880275 scopus 로고    scopus 로고
    • Burkholderiales ord
    • nov, Garrity GM, Brenner DJ, Krieg NR, Staley JT, Second Edition, Part C, Springer, New York
    • Garrity GM, Bell JA, Lilburn T. Order I. Burkholderiales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.
    • (2005) Bergey's Manual of Systematic Bacteriology , vol.2 , pp. 575
    • Garrity, G.M.1    Bell, J.A.2    Lilburn, T.3    Order, I.4
  • 30
    • 33747880275 scopus 로고    scopus 로고
    • Burkholderiaceae fam
    • nov, Garrity GM, Brenner DJ, Krieg NR, Staley JT, Second Edition, Part C, Springer, New York
    • Garrity GM, Bell JA, Lilburn T. Family I. Burkholderiaceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.
    • (2005) Bergey's Manual of Systematic Bacteriology , vol.2 , pp. 575
    • Garrity, G.M.1    Bell, J.A.2    Lilburn, T.3    Family, I.4
  • 31
    • 84859079960 scopus 로고    scopus 로고
    • BAuA. Classification of bacteria and archaea in risk groups, TRBA
    • BAuA. Classification of bacteria and archaea in risk groups. http://www.baua.de. TRBA 2010; 466:172.
    • (2010) , vol.466 , pp. 172
  • 33
    • 84859058285 scopus 로고    scopus 로고
    • The DOE Joint Genome Institute
    • The DOE Joint Genome Institute. www.jgi.doe.gov
  • 34
    • 84859094712 scopus 로고    scopus 로고
    • Phrap and Phred for Windows. MacOS, Linux, and Unix
    • Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
  • 35
    • 33751109989 scopus 로고    scopus 로고
    • Finishing repeat regions automatically with Dupfinisher
    • Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26-29, 2006
    • Cliff S. Han, Patrick Chain. 2006. Finishing repeat regions automatically with Dupfinisher. Proceeding of the 2006 international conference on bioinformatics & computational biology. Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26-29, 2006: 141-146.
    • (2006) Proceeding of the 2006 International Conference On Bioinformatics & Computational Biology , pp. 141-146
    • Han, C.S.1    Chain, P.2
  • 36
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • PubMed
    • Delcher AL, Bratke K, Powers E, Salzberg S. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673-679. PubMed http://dx.doi.org/10.1093/bioinformatics/btm009
    • (2007) Bioinformatics , vol.23 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.2    Powers, E.3    Salzberg, S.4
  • 37
    • 0032900737 scopus 로고    scopus 로고
    • CRITICA: Coding region identification tool invoking comparative analysis
    • PubMed
    • Badger JH, Olsen GJ. CRITICA: Coding region identification tool invoking comparative analysis. Mol Biol Evol 1999; 16:512-524. PubMed
    • (1999) Mol Biol Evol , vol.16 , pp. 512-524
    • Badger, J.H.1    Olsen, G.J.2
  • 38
    • 0030854739 scopus 로고    scopus 로고
    • TRNASCAN-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • PubMed
    • 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 http://dx.doi.org/10.1093/nar/25.5.955
    • (1997) Nucleic Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 39
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • PubMed
    • Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 2001; 305:567-580. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315
    • (2001) J Mol Biol , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.L.4
  • 40
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • PubMed
    • Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028
    • (2004) J Mol Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    von Heijne, G.3    Brunak, S.4
  • 41
    • 0028887837 scopus 로고
    • Taxonomic note: Implementation of the provisional status Candidatus for incompletely described procaryotes
    • PubMed
    • Murray RGE, Stackebrandt E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int J Syst Bacteriol 1995; 45:186-187. PubMed http://dx.doi.org/10.1099/00207713-45-1-186
    • (1995) Int J Syst Bacteriol , vol.45 , pp. 186-187
    • Murray, R.G.E.1    Stackebrandt, E.2
  • 42
    • 0036362507 scopus 로고    scopus 로고
    • A molecular approach to the tangled intrageneric relationships underlying phylogeny in Euplotes (Ciliophora, Spirotrichea)
    • PubMed
    • Petroni G, Dini F, Verni F, Rosati G. A molecular approach to the tangled intrageneric relationships underlying phylogeny in Euplotes (Ciliophora, Spirotrichea). Mol Phylogenet Evol 2002; 22:118-130. PubMed http://dx.doi.org/10.1006/mpev.2001.1030
    • (2002) Mol Phylogenet Evol , vol.22 , pp. 118-130
    • Petroni, G.1    Dini, F.2    Verni, F.3    Rosati, G.4
  • 43
    • 33846127088 scopus 로고    scopus 로고
    • Endosymbiosis in statu nascendi: Close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria)
    • PubMed
    • Vannini C, Pöckl M, Petroni G, Wu QL, Lang E, Stackebrandt E, Schrallhammer M, Richardson PM, Hahn MW. Endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living Polynucleobacter strains (Betaproteobacteria). Environ Microbiol 2007; 9:347-359. PubMed http://dx.doi.org/10.1111/j.1462-2920.2006.01144.x
    • (2007) Environ Microbiol , vol.9 , pp. 347-359
    • Vannini, C.1    Pöckl, M.2    Petroni, G.3    Wu, Q.L.4    Lang, E.5    Stackebrandt, E.6    Schrallhammer, M.7    Richardson, P.M.8    Hahn, M.W.9
  • 44
    • 84859058287 scopus 로고    scopus 로고
    • genome-to-genome distance calculator
    • genome-to-genome distance calculator. http://ggdc.gbdp.org
  • 45
    • 77952891045 scopus 로고    scopus 로고
    • Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
    • PubMed
    • Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142-148. PubMed http://dx.doi.org/10.4056/sigs.541628
    • (2010) Stand Genomic Sci , vol.2 , pp. 142-148
    • Auch, A.F.1    Klenk, H.P.2    Göker, M.3
  • 46
    • 77952891913 scopus 로고    scopus 로고
    • Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
    • PubMed
    • Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117-134. PubMed http://dx.doi.org/10.4056/sigs.531120
    • (2010) Stand Genomic Sci , vol.2 , pp. 117-134
    • Auch, A.F.1    von Jan, M.2    Klenk, H.P.3    Göker, M.4


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