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Volumn 7, Issue 4, 2016, Pages

Genomes of abundant and widespread viruses from the deep ocean

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTEROIDETES; BIOGEOCHEMISTRY; BIOMASS; CANDIDATUS PELAGIBACTER; CONTROLLED STUDY; DEEP SEA; DELTAPROTEOBACTERIA; DNA PURIFICATION; GAMMAPROTEOBACTERIA; HYDROTHERMAL VENT; LIFESTYLE; LYSOGENIZATION; METAGENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; PUNICEISPIRILLUM; TAXONOMY; VIRUS ASSEMBLY; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS STRAIN; BACTERIOPHAGE; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PROPHAGE; SEA; SEQUENCE HOMOLOGY; SYNTENY;

EID: 84986586972     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00805-16     Document Type: Article
Times cited : (72)

References (58)
  • 1
    • 34250813023 scopus 로고    scopus 로고
    • Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems
    • Corinaldesi C, Dell’Anno A, Danovaro R 2007. Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems. Limnol Oceangr 52:508-516. http://dx.doi.org/10.4319/lo.2007.52.2.0508
    • (2007) Limnol Oceangr , vol.52 , pp. 508-516
    • Corinaldesi, C.1    Dell’Anno, A.2    Danovaro, R.3
  • 2
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses—major players in the global ecosystem
    • Suttle CA 2007. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5:801-812. http://dx.doi.org/10.1038/nrmicro1750
    • (2007) Nat Rev Microbiol , vol.5 , pp. 801-812
    • Suttle, C.A.1
  • 9
    • 84897599619 scopus 로고    scopus 로고
    • Evidence for metaviromic islands in marine phages
    • Mizuno CM, Ghai R, Rodriguez-Valera F 2014. Evidence for metaviromic islands in marine phages. Front Microbiol 5:27. http://dx.doi.org/10.3389/fmicb.2014.00027
    • (2014) Front Microbiol , vol.5 , pp. 27
    • Mizuno, C.M.1    Ghai, R.2    Rodriguez-Valera, F.3
  • 12
    • 79960560896 scopus 로고    scopus 로고
    • Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea
    • Brochier-Armanet C, Deschamps P, López-García P, Zivanovic Y, Rodríguez-Valera F, Moreira D 2011. Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. ISME J 5:1291-1302. http://dx.doi.org/10.1038/ismej.2011.16
    • (2011) ISME J , vol.5 , pp. 1291-1302
    • Brochier-Armanet, C.1    Deschamps, P.2    López-García, P.3    Zivanovic, Y.4    Rodríguez-Valera, F.5    Moreira, D.6
  • 13
    • 84926123404 scopus 로고    scopus 로고
    • Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota
    • Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P 2014. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota. Genome Biol Evol 6:1549-1563. http://dx.doi.org/10.1093/gbe/evu127
    • (2014) Genome Biol Evol , vol.6 , pp. 1549-1563
    • Deschamps, P.1    Zivanovic, Y.2    Moreira, D.3    Rodriguez-Valera, F.4    López-García, P.5
  • 14
    • 49449099818 scopus 로고    scopus 로고
    • Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions
    • Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P 2008. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J 2:865-886. http://dx.doi.org/10.1038/ismej.2008.40
    • (2008) ISME J , vol.2 , pp. 865-886
    • Martin-Cuadrado, A.B.1    Rodriguez-Valera, F.2    Moreira, D.3    Alba, J.C.4    Ivars-Martínez, E.5    Henn, M.R.6    Talla, E.7    López-García, P.8
  • 15
    • 51649119779 scopus 로고    scopus 로고
    • Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton
    • Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D 2008. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ Microbiol 10: 2704-2717. http://dx.doi.org/10.1111/j.1462-2920.2008.01691.x
    • (2008) Environ Microbiol , vol.10 , pp. 2704-2717
    • Quaiser, A.1    López-García, P.2    Zivanovic, Y.3    Henn, M.R.4    Rodriguez-Valera, F.5    Moreira, D.6
  • 16
    • 0038377425 scopus 로고    scopus 로고
    • PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, “Pyrococcus abyssi”
    • Geslin C, Le Romancer M, Erauso G, Gaillard M, Perrot G, Prieur D 2003. PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, “Pyrococcus abyssi”. J Bacteriol 185:3888-3894. http://dx.doi.org/10.1128/JB.185.13.3888-3894.2003
    • (2003) J Bacteriol , vol.185 , pp. 3888-3894
    • Geslin, C.1    Le Romancer, M.2    Erauso, G.3    Gaillard, M.4    Perrot, G.5    Prieur, D.6
  • 18
    • 84922003801 scopus 로고    scopus 로고
    • Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp
    • Yoshida M, Yoshida-Takashima Y, Nunoura T, Takai K 2015. Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp. Extremophiles 19:49-58. http://dx.doi.org/10.1007/s00792-014-0702-5
    • (2015) Extremophiles , vol.19 , pp. 49-58
    • Yoshida, M.1    Yoshida-Takashima, Y.2    Nunoura, T.3    Takai, K.4
  • 19
    • 84864758161 scopus 로고    scopus 로고
    • Dynamic modulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature
    • Jian H, Xu J, Xiao X, Wang F 2012. Dynamic modulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature. PLoS One 7:e41578. http://dx.doi.org/10.1371/journal.pone.0041578
    • (2012) Plos One , pp. 7
    • Jian, H.1    Xu, J.2    Xiao, X.3    Wang, F.4
  • 20
    • 84874530236 scopus 로고    scopus 로고
    • The Pacific Ocean virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology
    • Hurwitz BL, Sullivan MB 2013. The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 8:e57355. http://dx.doi.org/10.1371/journal.pone.0057355
    • (2013) Plos One , pp. 8
    • Hurwitz, B.L.1    Sullivan, M.B.2
  • 21
    • 84903527526 scopus 로고    scopus 로고
    • Comparison of deep-water viromes from the Atlantic Ocean and the Mediterranean Sea
    • Winter C, Garcia JA, Weinbauer MG, DuBow MS, Herndl GJ 2014. Comparison of deep-water viromes from the Atlantic Ocean and the Mediterranean Sea. PLoS One 9:e100600. http://dx.doi.org/10.1371/journal.pone.0100600
    • (2014) Plos One , pp. 9
    • Winter, C.1    Garcia, J.A.2    Weinbauer, M.G.3    Dubow, M.S.4    Herndl, G.J.5
  • 22
    • 84874520341 scopus 로고    scopus 로고
    • Metagenomic analysis of viral communities in (Hado)pelagic sediments
    • Yoshida M, Takaki Y, Eitoku M, Nunoura T, Takai K 2013. Metagenomic analysis of viral communities in (hado)pelagic sediments. PLoS One 8:e57271. http://dx.doi.org/10.1371/journal.pone.0057271
    • (2013) Plos One , pp. 8
    • Yoshida, M.1    Takaki, Y.2    Eitoku, M.3    Nunoura, T.4    Takai, K.5
  • 23
    • 84921568760 scopus 로고    scopus 로고
    • Depth-stratified functional and taxonomic niche specialization in the “core” and “flexible” Pacific Ocean virome
    • Hurwitz BL, Brum JR, Sullivan MB 2015. Depth-stratified functional and taxonomic niche specialization in the “core” and “flexible” Pacific Ocean virome. ISME J 9:472-484. http://dx.doi.org/10.1038/ismej.2014.143
    • (2015) ISME J , vol.9 , pp. 472-484
    • Hurwitz, B.L.1    Brum, J.R.2    Sullivan, M.B.3
  • 24
    • 84892736640 scopus 로고    scopus 로고
    • Expanding the marine virosphere using metagenomics
    • Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R 2013. Expanding the marine virosphere using metagenomics. PLoS Genet 9:e1003987. http://dx.doi.org/10.1371/journal.pgen.1003987
    • (2013) Plos Genet , pp. 9
    • Mizuno, C.M.1    Rodriguez-Valera, F.2    Kimes, N.E.3    Ghai, R.4
  • 26
    • 0035167322 scopus 로고    scopus 로고
    • Common origin of four diverse families of large eukaryotic DNA viruses
    • Iyer LM, Aravind L, Koonin EV 2001. Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 75:11720-11734. http://dx.doi.org/10.1128/JVI.75.23.11720-11734.2001
    • (2001) J Virol , vol.75 , pp. 11720-11734
    • Iyer, L.M.1    Aravind, L.2    Koonin, E.V.3
  • 28
    • 0033834072 scopus 로고    scopus 로고
    • Iridovirus homologues of cellular genes— implications for the molecular evolution of large DNA viruses
    • Tidona CA, Darai G 2000. Iridovirus homologues of cellular genes— implications for the molecular evolution of large DNA viruses. Virus Genes 21:77-81. http://dx.doi.org/10.1023/A:1008192616923
    • (2000) Virus Genes , vol.21 , pp. 77-81
    • Tidona, C.A.1    Darai, G.2
  • 30
    • 84880693152 scopus 로고    scopus 로고
    • Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans
    • Kang I, Oh H-M, Kang D, Cho J-C 2013. Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proc Natl Acad Sci U S A 110:12343-12348. http://dx.doi.org/10.1073/pnas.1219930110
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 12343-12348
    • Kang, I.1    Oh, H.-M.2    Kang, D.3    Cho, J.-C.4
  • 33
    • 84963785503 scopus 로고    scopus 로고
    • Computational approaches to predict bacteriophage-host relationships
    • Edwards RA, McNair K, Faust K, Raes J, Dutilh BE 2016. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol Rev 40:258-272 http://dx.doi.org/10.1093/femsre/fuv048
    • (2016) FEMS Microbiol Rev , vol.40 , pp. 258-272
    • Edwards, R.A.1    McNair, K.2    Faust, K.3    Raes, J.4    Dutilh, B.E.5
  • 37
    • 84891160721 scopus 로고    scopus 로고
    • Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone
    • Ganesh S, Parris DJ, DeLong EF, Stewart FJ 2014. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J 8:187-211. http://dx.doi.org/10.1038/ismej.2013.144
    • (2014) ISME J , vol.8 , pp. 187-211
    • Ganesh, S.1    Parris, D.J.2    Delong, E.F.3    Stewart, F.J.4
  • 40
    • 0042572533 scopus 로고    scopus 로고
    • Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters
    • Weinbauer MG, Brettar I, Höfle MG 2003. Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnol Oceanogr 48:1457-1465. http://dx.doi.org/10.4319/lo.2003.48.4.1457
    • (2003) Limnol Oceanogr , vol.48 , pp. 1457-1465
    • Weinbauer, M.G.1    Brettar, I.2    Höfle, M.G.3
  • 42
    • 0030619262 scopus 로고    scopus 로고
    • Widespread archaea and novel bacteria from the deep sea as shown by 16S rRNA gene sequences
    • Fuhrman J, Davis A 1997. Widespread archaea and novel bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Ser 150:275-285. http://dx.doi.org/10.3354/meps150275
    • (1997) Mar Ecol Prog Ser , vol.150 , pp. 275-285
    • Fuhrman, J.1    Davis, A.2
  • 43
    • 0001925746 scopus 로고
    • The great ocean conveyor
    • Broeker W 1991. The great ocean conveyor. Oceanography 4:79-89. http://dx.doi.org/10.5670/oceanog.1991.07
    • (1991) Oceanography , vol.4 , pp. 79-89
    • Broeker, W.1
  • 44
    • 72949103084 scopus 로고    scopus 로고
    • CO dehydrogenase genes found in metagenomic fosmid clones from the deep Mediterranean sea
    • Martin-Cuadrado AB, Ghai R, Gonzaga A, Rodriguez-Valera F 2009. CO dehydrogenase genes found in metagenomic fosmid clones from the deep Mediterranean sea. Appl Environ Microbiol 75:7436-7444. http://dx.doi.org/10.1128/AEM.01283-09
    • (2009) Appl Environ Microbiol , vol.75 , pp. 7436-7444
    • Martin-Cuadrado, A.B.1    Ghai, R.2    Gonzaga, A.3    Rodriguez-Valera, F.4
  • 45
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-829. http://dx.doi.org/10.1101/gr.074492.107
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 46
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 50
    • 79955391269 scopus 로고    scopus 로고
    • Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts
    • Kristensen DM, Cai X, Mushegian A 2011. Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts. J Bacteriol 193:1806-1814. http://dx.doi.org/10.1128/JB.01311-10
    • (2011) J Bacteriol , vol.193 , pp. 1806-1814
    • Kristensen, D.M.1    Cai, X.2    Mushegian, A.3
  • 51
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Söding J, Biegert A, Lupas AN 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244-W248. http://dx.doi.org/10.1093/nar/gki408
    • (2005) Nucleic Acids Res , vol.33 , pp. W244-W248
    • Söding, J.1    Biegert, A.2    Lupas, A.N.3
  • 52
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR 2011. Accelerated profile HMM searches. PLOS Comput Biol 7:e1002195. http://dx.doi.org/10.1371/journal.pcbi.1002195
    • (2011) PLOS Comput Biol , pp. 7
    • Eddy, S.R.1
  • 53
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461. http://dx.doi.org/10.1093/bioinformatics/btq461
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 54
    • 84934440243 scopus 로고    scopus 로고
    • MAFFT: Iterative refinement and addi-tional methods
    • Katoh K, Standley DM 2014. MAFFT: iterative refinement and addi-tional methods. Methods Mol Biol 1079:131-146. http://dx.doi.org/10.1007/978-1-62703-646-7_8
    • (2014) Methods Mol Biol , vol.1079 , pp. 131-146
    • Katoh, K.1    Standley, D.M.2
  • 55
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. http://dx.doi.org/10.1371/journal.pone.0009490
    • (2010) Plos One , pp. 5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 56
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (Version 3.2)
    • Felsenstein J 1989. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1


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