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Volumn 9, Issue , 2008, Pages

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; OLIGONUCLEOTIDE;

EID: 52949105789     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-420     Document Type: Article
Times cited : (25)

References (44)
  • 1
    • 33744804299 scopus 로고    scopus 로고
    • Metagenomic analysis of the human distal gut microbiome
    • 10.1126/science.1124234 16741115
    • Gill SR et al.: Metagenomic analysis of the human distal gut microbiome Science 2006, 312(5778):1355-9. 10.1126/science.1124234 16741115
    • (2006) Science , vol.312 , Issue.5778 , pp. 1355-1359
    • Gill, S.R.1
  • 2
    • 33845508443 scopus 로고    scopus 로고
    • Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host
    • 1661682 17132046 10.1371/journal.pbio.0040413
    • Sonnenburg JL Chen CT Gordon JI Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host PLoS Biol 2006, 4(12):e413. 1661682 17132046 10.1371/journal.pbio.0040413
    • (2006) PLoS Biol , vol.4 , Issue.12
    • Sonnenburg, J.L.1    Chen, C.T.2    Gordon, J.I.3
  • 3
    • 0034053843 scopus 로고    scopus 로고
    • Virioplankton: Viruses in aquatic ecosystems
    • 98987 10704475 10.1128/MMBR.64.1.69-114.2000
    • Wommack KE Colwell RR Virioplankton: Viruses in aquatic ecosystems Microbiol Mol Biol Rev 2000, 64(1):69-114. 98987 10704475 10.1128/ MMBR.64.1.69-114.2000
    • (2000) Microbiol Mol Biol Rev , vol.64 , Issue.1 , pp. 69-114
    • Wommack, K.E.1    Colwell, R.R.2
  • 4
    • 1642299836 scopus 로고    scopus 로고
    • Phage community dynamics in hot springs
    • 368299 15006788 10.1128/AEM.70.3.1633-1640.2004
    • Breitbart M et al.: Phage community dynamics in hot springs Appl Environ Microbiol 2004, 70(3):1633-40. 368299 15006788 10.1128/ AEM.70.3.1633-1640.2004
    • (2004) Appl Environ Microbiol , vol.70 , Issue.3 , pp. 1633-1640
    • Breitbart, M.1
  • 5
    • 0043197312 scopus 로고    scopus 로고
    • Phage as agents of lateral gene transfer
    • 10.1016/S1369-5274(03)00086-9 12941415
    • Canchaya C et al.: Phage as agents of lateral gene transfer Curr Opin Microbiol 2003, 6(4):417-24. 10.1016/S1369-5274(03)00086-9 12941415
    • (2003) Curr Opin Microbiol , vol.6 , Issue.4 , pp. 417-424
    • Canchaya, C.1
  • 6
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses-major players in the global ecosystem
    • 10.1038/nrmicro1750 17853907
    • Suttle CA Marine viruses-major players in the global ecosystem Nat Rev Microbiol 2007, 5(10):801-12. 10.1038/nrmicro1750 17853907
    • (2007) Nat Rev Microbiol , vol.5 , Issue.10 , pp. 801-812
    • Suttle, C.A.1
  • 7
    • 0842266354 scopus 로고    scopus 로고
    • Are viruses driving microbial diversification and diversity?
    • 10.1046/j.1462-2920.2003.00539.x 14686936
    • Weinbauer MG Rassoulzadegan F Are viruses driving microbial diversification and diversity? Environ Microbiol 2004, 6(1):1-11. 10.1046/j.1462-2920.2003.00539.x 14686936
    • (2004) Environ Microbiol , vol.6 , Issue.1 , pp. 1-11
    • Weinbauer, M.G.1    Rassoulzadegan, F.2
  • 8
    • 0038054297 scopus 로고    scopus 로고
    • The role played by viruses in the evolution of their hosts: A view based on informational protein phylogenies
    • 10.1016/S0923-2508(03)00066-4 12798227
    • Filee J Forterre P Laurent J The role played by viruses in the evolution of their hosts: A view based on informational protein phylogenies Res Microbiol 2003, 154(4):237-43. 10.1016/S0923-2508(03)00066-4 12798227
    • (2003) Res Microbiol , vol.154 , Issue.4 , pp. 237-243
    • Filee, J.1    Forterre, P.2    Laurent, J.3
  • 9
    • 0037195156 scopus 로고    scopus 로고
    • Genomic analysis of uncultured marine viral communities
    • 137870 12384570 10.1073/pnas.202488399
    • Breitbart M et al.: Genomic analysis of uncultured marine viral communities Proc Natl Acad Sci USA 2002, 99(22):14250-5. 137870 12384570 10.1073/pnas.202488399
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.22 , pp. 14250-14255
    • Breitbart, M.1
  • 10
    • 39049150896 scopus 로고    scopus 로고
    • A bacterial metapopulation adapts locally to phage predation despite global dispersal
    • 2203627 18077539 10.1101/gr.6835308
    • Kunin V et al.: A bacterial metapopulation adapts locally to phage predation despite global dispersal Genome Res 2008, 18(2):293-7. 2203627 18077539 10.1101/gr.6835308
    • (2008) Genome Res , vol.18 , Issue.2 , pp. 293-297
    • Kunin, V.1
  • 11
    • 38449087833 scopus 로고    scopus 로고
    • Metagenomic characterization of Chesapeake Bay virioplankton
    • 2168038 17921274 10.1128/AEM.00938-07
    • Bench SR et al.: Metagenomic characterization of Chesapeake Bay virioplankton Appl Environ Microbiol 2007, 73(23):7629-41. 2168038 17921274 10.1128/AEM.00938-07
    • (2007) Appl Environ Microbiol , vol.73 , Issue.23 , pp. 7629-7641
    • Bench, S.R.1
  • 12
    • 46949106154 scopus 로고    scopus 로고
    • Assembly of viral metagenomes from yellowstone hot springs
    • 10.1128/AEM.02598-07 18441115
    • Schoenfeld T et al.: Assembly of viral metagenomes from yellowstone hot springs Appl Environ Microbiol 2008, 74(13):4164-74. 10.1128/ AEM.02598-07 18441115
    • (2008) Appl Environ Microbiol , vol.74 , Issue.13 , pp. 4164-4174
    • Schoenfeld, T.1
  • 13
    • 0141891348 scopus 로고    scopus 로고
    • Metagenomic analyses of an uncultured viral community from human feces
    • 225035 14526037 10.1128/JB.185.20.6220-6223.2003
    • Breitbart M et al.: Metagenomic analyses of an uncultured viral community from human feces J Bacteriol 2003, 185(20):6220-3. 225035 14526037 10.1128/JB.185.20.6220-6223.2003
    • (2003) J Bacteriol , vol.185 , Issue.20 , pp. 6220-6223
    • Breitbart, M.1
  • 14
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • 2231712
    • Altschul SF et al.: Basic local alignment search tool J Mol Biol 1990, 215(3):403-10. 2231712
    • (1990) J Mol Biol , vol.215 , Issue.3 , pp. 403-410
    • Altschul, S.F.1
  • 15
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • 420360 12566393 10.1101/gr.335003
    • Pride DT et al.: Evolutionary implications of microbial genome tetranucleotide frequency biases Genome Res 2003, 13(2):145-58. 420360 12566393 10.1101/gr.335003
    • (2003) Genome Res , vol.13 , Issue.2 , pp. 145-158
    • Pride, D.T.1
  • 16
    • 0028028028 scopus 로고
    • Computational DNA sequence analysis
    • 10.1146/annurev.mi.48.100194.003155 7826021
    • Karlin S Cardon LR Computational DNA sequence analysis Annu Rev Microbiol 1994, 48:619-54. 10.1146/annurev.mi.48.100194.003155 7826021
    • (1994) Annu Rev Microbiol , vol.48 , pp. 619-654
    • Karlin, S.1    Cardon, L.R.2
  • 17
    • 0026502711 scopus 로고
    • Over- and under-representation of short oligonucleotides in DNA sequences
    • 48449 1741388 10.1073/pnas.89.4.1358
    • Burge C Campbell AM Karlin S Over- and under-representation of short oligonucleotides in DNA sequences Proc Natl Acad Sci USA 1992, 89(4):1358-62. 48449 1741388 10.1073/pnas.89.4.1358
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.4 , pp. 1358-1362
    • Burge, C.1    Campbell, A.M.2    Karlin, S.3
  • 18
    • 13244279471 scopus 로고    scopus 로고
    • Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns
    • 487896 15239845 10.1186/1471-2105-5-90
    • Reva ON Tummler B Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns BMC Bioinformatics 2004, 5:90. 487896 15239845 10.1186/ 1471-2105-5-90
    • (2004) BMC Bioinformatics , vol.5 , pp. 90
    • Reva, O.N.1    Tummler, B.2
  • 19
    • 0002576679 scopus 로고    scopus 로고
    • Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis
    • 10.1166/gl.2002.003
    • Pride DT Blaser MJ Identification of horizontally acquired genetic elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis Genome Letters 2002, 1(1):2-15. 10.1166/gl.2002.003
    • (2002) Genome Letters , vol.1 , Issue.1 , pp. 2-15
    • Pride, D.T.1    Blaser, M.J.2
  • 20
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • 10.1038/nmeth976 17179938
    • McHardy AC et al.: Accurate phylogenetic classification of variable-length DNA fragments Nat Methods 2007, 4(1):63-72. 10.1038/ nmeth976 17179938
    • (2007) Nat Methods , vol.4 , Issue.1 , pp. 63-72
    • McHardy, A.C.1
  • 21
    • 52949087876 scopus 로고    scopus 로고
    • Manual of Clinical Microbiology
    • Buchen-Osmond C ed ASM Press: Washington DC Buchen-Osmond C 8
    • Buchen-Osmond C ed Manual of Clinical Microbiology Taxonomy and Classification of Viruses ASM Press: Washington DC Buchen-Osmond C 8 2003, 2:1217-1226.
    • (2003) Taxonomy and Classification of Viruses , vol.2 , pp. 1217-1226
  • 22
    • 0036719291 scopus 로고    scopus 로고
    • Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches
    • 135278 12169615 10.1128/JB.184.17.4891-4905.2002
    • Lawrence JG Hatfull GF Hendrix RW Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches J Bacteriol 2002, 184(17):4891-905. 135278 12169615 10.1128/JB.184.17.4891-4905.2002
    • (2002) J Bacteriol , vol.184 , Issue.17 , pp. 4891-4905
    • Lawrence, J.G.1    Hatfull, G.F.2    Hendrix, R.W.3
  • 23
    • 14944359669 scopus 로고    scopus 로고
    • Effects of culturing on the population structure of a hyperthermophilic virus
    • 10.1007/s00248-004-0246-9 15696389
    • Snyder JC et al.: Effects of culturing on the population structure of a hyperthermophilic virus Microb Ecol 2004, 48(4):561-6. 10.1007/ s00248-004-0246-9 15696389
    • (2004) Microb Ecol , vol.48 , Issue.4 , pp. 561-566
    • Snyder, J.C.1
  • 24
    • 0036330981 scopus 로고    scopus 로고
    • The Phage Proteomic Tree: A genome-based taxonomy for phage
    • 135240 12142423 10.1128/JB.184.16.4529-4535.2002
    • Rohwer F Edwards R The Phage Proteomic Tree: A genome-based taxonomy for phage J Bacteriol 2002, 184(16):4529-35. 135240 12142423 10.1128/ JB.184.16.4529-4535.2002
    • (2002) J Bacteriol , vol.184 , Issue.16 , pp. 4529-4535
    • Rohwer, F.1    Edwards, R.2
  • 25
    • 32044436032 scopus 로고    scopus 로고
    • Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses
    • 1360066 16417644 10.1186/1471-2164-7-8
    • Pride DT Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses BMC Genomics 2006, 7:8. 1360066 16417644 10.1186/1471-2164-7-8
    • (2006) BMC Genomics , vol.7 , pp. 8
    • Pride, D.T.1
  • 27
    • 0016793389 scopus 로고
    • Isolation and characterization of a bacteriophage infectious to an extreme thermophile, Thermus thermophilus HB8
    • 354612 1142476
    • Y Oshima T Isolation and characterization of a bacteriophage infectious to an extreme thermophile, Thermus thermophilus HB8 J Virol 1975, 15(6):1449-53. 354612 1142476
    • (1975) J Virol , vol.15 , Issue.6 , pp. 1449-1453
    • Sakaki, Y.1    Oshima, T.2
  • 28
    • 33645019226 scopus 로고    scopus 로고
    • Isolation and characterization of Thermus bacteriophages
    • 10.1007/s00705-005-0667-x 16308675
    • Yu MX Slater MR Ackermann HW Isolation and characterization of Thermus bacteriophages Arch Virol 2006, 151(4):663-79. 10.1007/s00705-005-0667-x 16308675
    • (2006) Arch Virol , vol.151 , Issue.4 , pp. 663-679
    • Yu, M.X.1    Slater, M.R.2    Ackermann, H.W.3
  • 29
    • 33645087247 scopus 로고    scopus 로고
    • Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life
    • 10.1016/j.virusres.2006.01.007 16503363
    • Prangishvili D Garrett RA Koonin EV Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life Virus Res 2006, 117(1):52-67. 10.1016/j.virusres.2006.01.007 16503363
    • (2006) Virus Res , vol.117 , Issue.1 , pp. 52-67
    • Prangishvili, D.1    Garrett, R.A.2    Koonin, E.V.3
  • 30
    • 52949122831 scopus 로고    scopus 로고
    • Geothermal Biology and Geochemistry in Yellowstone National Park
    • Inskeep WP McDermott TR eds Proceedings of the Thermal Biology Institute Workshop Fournier RO
    • Inskeep WP McDermott TR eds Geothermal Biology and Geochemistry in Yellowstone National Park Geochemistry and Dynamics of the Yellowstone National Park Hydrothermal System Proceedings of the Thermal Biology Institute Workshop Fournier RO 2005.
    • (2005) Geochemistry and Dynamics of the Yellowstone National Park Hydrothermal System
  • 31
    • 0028308089 scopus 로고
    • Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park
    • 201609 7518219
    • Reysenbach AL Wickham GS Pace NR Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park Appl Environ Microbiol 1994, 60(6):2113-9. 201609 7518219
    • (1994) Appl Environ Microbiol , vol.60 , Issue.6 , pp. 2113-2119
    • Reysenbach, A.L.1    Wickham, G.S.2    Pace, N.R.3
  • 32
    • 0036793770 scopus 로고    scopus 로고
    • Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park
    • 126385 12324363 10.1128/AEM.68.10.5123-5135.2002
    • Blank CE Cady SL Pace NR Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park Appl Environ Microbiol 2002, 68(10):5123-35. 126385 12324363 10.1128/ AEM.68.10.5123-5135.2002
    • (2002) Appl Environ Microbiol , vol.68 , Issue.10 , pp. 5123-5135
    • Blank, C.E.1    Cady, S.L.2    Pace, N.R.3
  • 33
    • 0035512204 scopus 로고    scopus 로고
    • Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives
    • 93288 11679343 10.1128/AEM.67.11.5179-5189.2001
    • Jahnke LL et al.: Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives Appl Environ Microbiol 2001, 67(11):5179-89. 93288 11679343 10.1128/AEM.67.11.5179-5189.2001
    • (2001) Appl Environ Microbiol , vol.67 , Issue.11 , pp. 5179-5189
    • Jahnke, L.L.1
  • 34
    • 0022083127 scopus 로고
    • Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences
    • 241732 2409920
    • Stahl DA et al.: Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences Appl Environ Microbiol 1985, 49(6):1379-84. 241732 2409920
    • (1985) Appl Environ Microbiol , vol.49 , Issue.6 , pp. 1379-1384
    • Stahl, D.A.1
  • 35
    • 0022503208 scopus 로고
    • Isolation and preliminary taxonomic studies of Thermus strains isolated from Yellowstone National Park, USA
    • 3806053
    • Munster MJ et al.: Isolation and preliminary taxonomic studies of Thermus strains isolated from Yellowstone National Park, USA J Gen Microbiol 1986, 132(6):1677-83. 3806053
    • (1986) J Gen Microbiol , vol.132 , Issue.6 , pp. 1677-1683
    • Munster, M.J.1
  • 36
    • 52949093851 scopus 로고    scopus 로고
    • Microbial Diversity of Marine and Terrestrial Thermal Springs
    • Reysenbach AL Gotz D Yernool D eds Wiley Liss New York Reysenbach AL, Staley JT
    • Reysenbach AL Gotz D Yernool D eds Microbial Diversity of Marine and Terrestrial Thermal Springs Biodiversity of Microbial Life Wiley Liss New York Reysenbach AL, Staley JT 2002.
    • (2002) Biodiversity of Microbial Life
  • 37
    • 3843150551 scopus 로고    scopus 로고
    • Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles
    • 1470942 15280258 10.1534/genetics.104.026344
    • Friedman R Drake JW Hughes AL Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles Genetics 2004, 167(3):1507-12. 1470942 15280258 10.1534/genetics.104.026344
    • (2004) Genetics , vol.167 , Issue.3 , pp. 1507-1512
    • Friedman, R.1    Drake, J.W.2    Hughes, A.L.3
  • 38
    • 0242290154 scopus 로고    scopus 로고
    • Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content
    • 14604790 10.1016/S0378-1119(03)00660-7
    • Singer GA Hickey DA Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content Gene 2003, 317(1-2):39-47. 14604790 10.1016/S0378-1119(03)00660-7
    • (2003) Gene , vol.317 , Issue.1-2 , pp. 39-47
    • Singer, G.A.1    Hickey, D.A.2
  • 39
    • 2942590839 scopus 로고    scopus 로고
    • Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: A novel virus family, the Globuloviridae
    • 10.1016/j.virol.2004.03.002 15193919
    • Haring M et al.: Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: A novel virus family, the Globuloviridae Virology 2004, 323(2):233-42. 10.1016/j.virol.2004.03.002 15193919
    • (2004) Virology , vol.323 , Issue.2 , pp. 233-242
    • Haring, M.1
  • 40
    • 33751059692 scopus 로고    scopus 로고
    • The marine viromes of four oceanic regions
    • 1634881 17090214 10.1371/journal.pbio.0040368
    • Angly FE et al.: The marine viromes of four oceanic regions PLoS Biol 2006, 4(11):e368. 1634881 17090214 10.1371/journal.pbio.0040368
    • (2006) PLoS Biol , vol.4 , Issue.11
    • Angly, F.E.1
  • 41
    • 0021109593 scopus 로고
    • A Markov analysis of DNA sequences
    • 10.1016/0022-5193(83)90251-5 6316035
    • Almagor H et al.: A Markov analysis of DNA sequences J Theor Biol 1983, 104(4):633-45. 10.1016/0022-5193(83)90251-5 6316035
    • (1983) J Theor Biol , vol.104 , Issue.4 , pp. 633-645
    • Almagor, H.1
  • 44
    • 0030203863 scopus 로고    scopus 로고
    • TreeView: An application to display phylogenetic trees on personal computers
    • 8902363
    • Page RD TreeView: An application to display phylogenetic trees on personal computers Comput Appl Biosci 1996, 12(4):357-8. 8902363
    • (1996) Comput Appl Biosci , vol.12 , Issue.4 , pp. 357-358
    • Page, R.D.1


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