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Volumn 8, Issue 4, 2013, Pages

Assembly of a Marine Viral Metagenome after Physical Fractionation

Author keywords

[No Author keywords available]

Indexed keywords

CESIUM CHLORIDE; CONTIG; DNA POLYMERASE;

EID: 84875972917     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060604     Document Type: Article
Times cited : (19)

References (44)
  • 1
    • 83655191021 scopus 로고    scopus 로고
    • Marine Viruses: Truth or Dare
    • Breitbart M, (2012) Marine Viruses: Truth or Dare. Ann Rev Mar Sci 4: 425-448.
    • (2012) Ann Rev Mar Sci , vol.4 , pp. 425-448
    • Breitbart, M.1
  • 2
    • 0034053843 scopus 로고    scopus 로고
    • Virioplankton: viruses in aquatic ecosystems
    • Wommack KE, Colwell RR, (2000) Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64: 69-114.
    • (2000) Microbiol Mol Biol Rev , vol.64 , pp. 69-114
    • Wommack, K.E.1    Colwell, R.R.2
  • 3
    • 0034517760 scopus 로고    scopus 로고
    • Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments
    • Steward GF, Montiel JL, Azam F, (2000) Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments. Limnol Oceanogr 45: 1697-1706.
    • (2000) Limnol Oceanogr , vol.45 , pp. 1697-1706
    • Steward, G.F.1    Montiel, J.L.2    Azam, F.3
  • 4
    • 21344461027 scopus 로고    scopus 로고
    • Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations
    • Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW, (2005) Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 3: 790-806.
    • (2005) PLoS Biol , vol.3 , pp. 790-806
    • Sullivan, M.B.1    Coleman, M.L.2    Weigele, P.3    Rohwer, F.4    Chisholm, S.W.5
  • 5
    • 0036692453 scopus 로고    scopus 로고
    • Isolation and characterization of a virus that infects Emiliania huxleyi (Haptophyta)
    • Castberg T, Thyrhaug R, Larsen A, Sandaa R-A, Heldal M, et al. (2002) Isolation and characterization of a virus that infects Emiliania huxleyi (Haptophyta). J Phycol 38: 767-774.
    • (2002) J Phycol , vol.38 , pp. 767-774
    • Castberg, T.1    Thyrhaug, R.2    Larsen, A.3    Sandaa, R.-A.4    Heldal, M.5
  • 6
    • 17644410730 scopus 로고    scopus 로고
    • The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains
    • Mann NH, Clokie MRJ, Millard A, Cook A, Wilson WH, et al. (2005) The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains. J Bacteriol 187: 3188-3200.
    • (2005) J Bacteriol , vol.187 , pp. 3188-3200
    • Mann, N.H.1    Clokie, M.R.J.2    Millard, A.3    Cook, A.4    Wilson, W.H.5
  • 7
    • 0036181778 scopus 로고    scopus 로고
    • Exploring prokaryotic diversity in the genomic era
    • reviews0003.1-reviews0003.8
    • Hugenholtz P, (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3: reviews0003.1-0003.8.
    • (2002) Genome Biol , vol.3
    • Hugenholtz, P.1
  • 12
    • 1642363900 scopus 로고    scopus 로고
    • Diversity and population structure of a near-shore marine-sediment viral community
    • Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, et al. (2004) Diversity and population structure of a near-shore marine-sediment viral community. Proc Roy Soc B 271: 565-574.
    • (2004) Proc Roy Soc B , vol.271 , pp. 565-574
    • Breitbart, M.1    Felts, B.2    Kelley, S.3    Mahaffy, J.M.4    Nulton, J.5
  • 15
    • 33745513227 scopus 로고    scopus 로고
    • Metagenomic analysis of coastal RNA virus communities
    • Culley AI, Lang AS, Suttle CA, (2006) Metagenomic analysis of coastal RNA virus communities. Science 312: 1795-1798.
    • (2006) Science , vol.312 , pp. 1795-1798
    • Culley, A.I.1    Lang, A.S.2    Suttle, C.A.3
  • 16
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1    Chapman, J.2    Hugenholtz, P.3    Allen, E.E.4    Ram, R.J.5
  • 17
    • 33748299286 scopus 로고    scopus 로고
    • Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
    • Legault BA, Lopez-Lopez A, Alba-Casado JC, Doolittle WF, Bolhuis H, et al. (2006) Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 7: 171.
    • (2006) BMC Genomics , vol.7 , pp. 171
    • Legault, B.A.1    Lopez-Lopez, A.2    Alba-Casado, J.C.3    Doolittle, W.F.4    Bolhuis, H.5
  • 19
    • 55449131166 scopus 로고    scopus 로고
    • Bioinformatics for whole-genome shotgun sequencing of microbial communities
    • Chen K, Pachter L, (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 1: 0106-0112.
    • (2005) PLoS Comput Biol , vol.1 , pp. 0106-0112
    • Chen, K.1    Pachter, L.2
  • 20
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 21
    • 34249933858 scopus 로고    scopus 로고
    • What's the 'meta' with metagenomics?
    • Steward GF, Rappé MS, (2007) What's the 'meta' with metagenomics? ISME J 1: 100-102.
    • (2007) ISME J , vol.1 , pp. 100-102
    • Steward, G.F.1    Rappé, M.S.2
  • 22
    • 41049102726 scopus 로고    scopus 로고
    • Divide and conquer: enriching environmental sequencing data
    • Bergeron A, Belcaid M, Steward GF, Poisson G, (2007) Divide and conquer: enriching environmental sequencing data. PLoS ONE 2: e830.
    • (2007) PLoS ONE , vol.2
    • Bergeron, A.1    Belcaid, M.2    Steward, G.F.3    Poisson, G.4
  • 23
    • 79955416724 scopus 로고    scopus 로고
    • Physical fractionation of aquatic viral assemblages
    • Brum JR, Steward GF, (2011) Physical fractionation of aquatic viral assemblages. Limnol Oceanogr Methods 9: 150-163.
    • (2011) Limnol Oceanogr Methods , vol.9 , pp. 150-163
    • Brum, J.R.1    Steward, G.F.2
  • 24
    • 23044527038 scopus 로고    scopus 로고
    • Fingerprinting viral assemblages by pulsed field gel electrophoresis (PFGE)
    • Paul JH, editor, New York: Academic Press
    • Steward GF (2001) Fingerprinting viral assemblages by pulsed field gel electrophoresis (PFGE). In: Paul JH, editor. Methods in Microbiology, Volume 30. New York: Academic Press. 85-103.
    • (2001) Methods in Microbiology , vol.30 , pp. 85-103
    • Steward, G.F.1
  • 25
    • 0001679973 scopus 로고    scopus 로고
    • Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria
    • Noble RT, Fuhrman JA, (1998) Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14: 113-118.
    • (1998) Aquat Microb Ecol , vol.14 , pp. 113-118
    • Noble, R.T.1    Fuhrman, J.A.2
  • 26
    • 29244484220 scopus 로고    scopus 로고
    • Concentration, production, and turnover of viruses and dissolved DNA pools at Station ALOHA, North Pacific Subtropical Gyre
    • Brum JR, (2005) Concentration, production, and turnover of viruses and dissolved DNA pools at Station ALOHA, North Pacific Subtropical Gyre. Aquat Microb Ecol 41: 103-113.
    • (2005) Aquat Microb Ecol , vol.41 , pp. 103-113
    • Brum, J.R.1
  • 27
    • 78649707158 scopus 로고    scopus 로고
    • Multiple displacement amplification compromises quantitative analysis of metagenomes
    • Yilmaz S, Allgaier M, Hugenholtz P, (2010) Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7: 943-944.
    • (2010) Nat Methods , vol.7 , pp. 943-944
    • Yilmaz, S.1    Allgaier, M.2    Hugenholtz, P.3
  • 29
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 30
    • 84864387036 scopus 로고    scopus 로고
    • Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes
    • Ignacio-Espinoza JC, Sullivan MB, (2012) Phylogenomics of T4 cyanophages: lateral gene transfer in the 'core' and origins of host genes. Environ Microbiol 14: 2113-2126.
    • (2012) Environ Microbiol , vol.14 , pp. 2113-2126
    • Ignacio-Espinoza, J.C.1    Sullivan, M.B.2
  • 31
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
    • Stamatakis A, Ludwig T, Meier H, (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 32
    • 0033214628 scopus 로고    scopus 로고
    • Heuristic approach to deriving models for gene finding
    • Besemer J, Borodovsky M, (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27: 3911-3920.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 33
    • 15444372597 scopus 로고    scopus 로고
    • Genomic analysis of bacteriophage phi JL001: insights into its interaction with a sponge-associated alpha-proteobacterium
    • Lohr JE, Chen F, Hill RT, (2005) Genomic analysis of bacteriophage phi JL001: insights into its interaction with a sponge-associated alpha-proteobacterium. Appl Environ Microbiol 71: 1598-1609.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 1598-1609
    • Lohr, J.E.1    Chen, F.2    Hill, R.T.3
  • 35
    • 78249280297 scopus 로고    scopus 로고
    • Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments
    • Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, et al. (2010) Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments. Environ Microbiol 12: 3035-3056.
    • (2010) Environ Microbiol , vol.12 , pp. 3035-3056
    • Sullivan, M.B.1    Huang, K.H.2    Ignacio-Espinoza, J.C.3    Berlin, A.M.4    Kelly, L.5
  • 36
    • 0036719291 scopus 로고    scopus 로고
    • Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches
    • Lawrence JG, Hatfull GF, Hendrix RW, (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 184: 4891-4905.
    • (2002) J Bacteriol , vol.184 , pp. 4891-4905
    • Lawrence, J.G.1    Hatfull, G.F.2    Hendrix, R.W.3
  • 37
    • 35948953592 scopus 로고    scopus 로고
    • Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
    • Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, et al. (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73: 7059-7066.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 7059-7066
    • Fierer, N.1    Breitbart, M.2    Nulton, J.3    Salamon, P.4    Lozupone, C.5
  • 38
    • 79958021198 scopus 로고    scopus 로고
    • Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning
    • Steward GF, Preston CM, (2011) Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning. Virol J 8: 287.
    • (2011) Virol J , vol.8 , pp. 287
    • Steward, G.F.1    Preston, C.M.2
  • 39
    • 34247489656 scopus 로고    scopus 로고
    • Mechanism of chimera formation during the Multiple Displacement Amplification reaction
    • Lasken R, Stockwell T, (2007) Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnol 7: 19.
    • (2007) BMC Biotechnol , vol.7 , pp. 19
    • Lasken, R.1    Stockwell, T.2
  • 40
    • 83155190998 scopus 로고    scopus 로고
    • Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses
    • Kim K-H, Bae J-W, (2011) Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 77: 7663-7668.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 7663-7668
    • Kim, K.-H.1    Bae, J.-W.2
  • 41
    • 84865720549 scopus 로고    scopus 로고
    • Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
    • Duhaime MBD, Deng L, Poulos BT, Sullivan MB, (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol 14: 2526-2537.
    • (2012) Environ Microbiol , vol.14 , pp. 2526-2537
    • Duhaime, M.B.D.1    Deng, L.2    Poulos, B.T.3    Sullivan, M.B.4
  • 42
    • 31544483932 scopus 로고    scopus 로고
    • Community genomics among stratified microbial assemblages in the ocean's interior
    • DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
    • (2006) Science , vol.311 , pp. 496-503
    • DeLong, E.F.1    Preston, C.M.2    Mincer, T.3    Rich, V.4    Hallam, S.J.5


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