메뉴 건너뛰기




Volumn 79, Issue 2, 2013, Pages 688-695

Reconstruction of novel cyanobacterial siphovirus genomes from mediterranean metagenomic fosmids

Author keywords

[No Author keywords available]

Indexed keywords

CONTIGS; DEEP CHLOROPHYLL MAXIMUMS; GENOME ARCHITECTURE; GENOMIC DNA; METAGENOMES; MICROBIAL COMMUNITY STRUCTURES; PHYLOGENETIC TREES; PICOCYANOBACTERIA; SAMPLE COLLECTION; SEQUENCE SIMILARITY; SYNECHOCOCCUS;

EID: 84871894692     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02742-12     Document Type: Article
Times cited : (29)

References (48)
  • 2
    • 84876484290 scopus 로고    scopus 로고
    • Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
    • doi:10.1111/j.1462-2920.2012.02836.x
    • Hurwitz BL, Deng L, Poulos BT, Sullivan MB. 2012. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ. Microbiol. doi:10.1111 /j.1462-2920.2012.02836.x.
    • (2012) Environ. Microbiol.
    • Hurwitz, B.L.1    Deng, L.2    Poulos, B.T.3    Sullivan, M.B.4
  • 4
    • 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 MB, 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.1    Deng, L.2    Poulos, B.T.3    Sullivan, M.B.4
  • 5
    • 84870665503 scopus 로고    scopus 로고
    • Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
    • doi:10.1016/j.virol.2012.09.036
    • Duhaime MB, Sullivan MB. 2012. Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology. doi:10.1016/j.virol.2012.09.036.
    • (2012) Virology
    • Duhaime, M.B.1    Sullivan, M.B.2
  • 10
    • 84855462375 scopus 로고    scopus 로고
    • Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea
    • Ngugi DK, Antunes A, Brune A, Stingl U. 2012. Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea. Mol. Ecol. 21:388-405.
    • (2012) Mol. Ecol. , vol.21 , pp. 388-405
    • Ngugi, D.K.1    Antunes, A.2    Brune, A.3    Stingl, U.4
  • 12
    • 0035403340 scopus 로고    scopus 로고
    • Distribution, isolation, host specificity, and diversity of cyanophages infecting marine Synechococcus spp
    • Lu J, Chen F, Hodson RE. 2001. Distribution, isolation, host specificity, and diversity of cyanophages infecting marine Synechococcus spp. in river estuaries. Appl. Environ. Microbiol. 67:3285-3290.
    • (2001) in river estuaries. Appl. Environ. Microbiol. , vol.67 , pp. 3285-3290
    • Lu, J.1    Chen, F.2    Hodson, R.E.3
  • 13
    • 0027802137 scopus 로고
    • Marine cyanophages infecting oceanic and coastal strains of Synechococcus: abundance, morphology, cross-infectivity and growth characteristics
    • Suttle CA. 1993. Marine cyanophages infecting oceanic and coastal strains of Synechococcus: abundance, morphology, cross-infectivity and growth characteristics. Mar. Ecol. Prog. Ser. 92:99-109.
    • (1993) Mar. Ecol. Prog. Ser. , vol.92 , pp. 99-109
    • Suttle, C.A.1
  • 14
    • 0027329223 scopus 로고
    • Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater
    • Waterbury JB, Valois FW. 1993. Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl. Environ. Microbiol. 59:3393-3399.
    • (1993) Appl. Environ. Microbiol , vol.59 , pp. 3393-3399
    • Waterbury, J.B.1    Valois, F.W.2
  • 15
    • 0027376914 scopus 로고
    • Isolation and molecular characterization of five marine cyanophages propagated on Synechococcus sp
    • Wilson WH, Joint IR, Carr NG, Mann NH. 1993. Isolation and molecular characterization of five marine cyanophages propagated on Synechococcus sp. strain WH7803. Appl. Environ. Microbiol. 59:3736-3743.
    • (1993) strain WH7803. Appl. Environ. Microbiol , vol.59 , pp. 3736-3743
    • Wilson, W.H.1    Joint, I.R.2    Carr, N.G.3    Mann, N.H.4
  • 16
    • 0036255283 scopus 로고    scopus 로고
    • Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages
    • Chen F, Lu J. 2002. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68:2589-2594.
    • (2002) Appl. Environ. Microbiol , vol.68 , pp. 2589-2594
    • Chen, F.1    Lu, J.2
  • 18
    • 69949104491 scopus 로고    scopus 로고
    • Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution
    • Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ. 2009. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environ. Microbiol. 11:2370-2387.
    • (2009) Environ. Microbiol , vol.11 , pp. 2370-2387
    • Millard, A.D.1    Zwirglmaier, K.2    Downey, M.J.3    Mann, N.H.4    Scanlan, D.J.5
  • 20
    • 21344461027 scopus 로고    scopus 로고
    • Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations
    • doi:10.1371/journal.pbio.0030144
    • Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. 2005. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 3:e144. doi:10.1371/journal.pbio.0030144.
    • (2005) PLoS Biol. 3
    • Sullivan, M.B.1    Coleman, M.L.2    Weigele, P.3    Rohwer, F.4    Chisholm, S.W.5
  • 24
    • 84856579879 scopus 로고    scopus 로고
    • Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges
    • Huang S, Wang K, Jiao N, Chen F. 2012. Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environ. Microbiol. 14:540-558.
    • (2012) Environ. Microbiol , vol.14 , pp. 540-558
    • Huang, S.1    Wang, K.2    Jiao, N.3    Chen, F.4
  • 27
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 28
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33:W244-W248.
    • (2005) Nucleic Acids Res. , vol.33
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 29
  • 30
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 31
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • doi:10.1371/journal.pone.0009490
    • Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. doi:10.1371/journal.pone.0009490.
    • (2010) PLoS One , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 32
    • 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
  • 33
    • 34250662138 scopus 로고    scopus 로고
    • The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    • Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8:172.
    • (2007) BMC Bioinformatics , vol.8 , pp. 172
    • Grissa, I.1    Vergnaud, G.2    Pourcel, C.3
  • 34
    • 33846975418 scopus 로고    scopus 로고
    • PILER-CR: fast and accurate identification of CRISPR repeats
    • Edgar R. 2007. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8:18.
    • (2007) BMC Bioinformatics , vol.8 , pp. 18
    • Edgar, R.1
  • 36
    • 0031761964 scopus 로고    scopus 로고
    • Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales
    • Maniloff J, Ackermann HW. 1998. Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales. Arch. Virol. 143:2051-2063.
    • (1998) Arch. Virol. , vol.143 , pp. 2051-2063
    • Maniloff, J.1    Ackermann, H.W.2
  • 38
    • 27744480467 scopus 로고    scopus 로고
    • Photosynthesis genes in marine viruses yield proteins during host infection
    • Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. 2005. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438:86-89.
    • (2005) Nature , vol.438 , pp. 86-89
    • Lindell, D.1    Jaffe, J.D.2    Johnson, Z.I.3    Church, G.M.4    Chisholm, S.W.5
  • 40
    • 0041736065 scopus 로고    scopus 로고
    • Marine ecosystems: bacterial photosynthesis genes in a virus
    • Mann NH, Cook A, Millard A, Bailey S, Clokie M. 2003. Marine ecosystems: bacterial photosynthesis genes in a virus. Nature 424:741-741.
    • (2003) Nature , vol.424 , pp. 741-741
    • Mann, N.H.1    Cook, A.2    Millard, A.3    Bailey, S.4    Clokie, M.5
  • 41
    • 3342929288 scopus 로고    scopus 로고
    • Genetic organization of the psbAD region in phages infecting marine Synechococcus strains
    • Millard A, Clokie MRJ, Shub DA, Mann NH. 2004. Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proc. Natl. Acad. Sci. U. S. A. 101:11007.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 11007
    • Millard, A.1    Clokie, M.R.J.2    Shub, D.A.3    Mann, N.H.4
  • 43
    • 84856523441 scopus 로고    scopus 로고
    • Identification of a bifunctional primase-polymerase domain of corynephage BFK20 replication protein gp43
    • Halgasova N, Mesarosova I, Bukovska G. 2012. Identification of a bifunctional primase-polymerase domain of corynephage BFK20 replication protein gp43. Virus Res. 163:454-460.
    • (2012) Virus Res. , vol.163 , pp. 454-460
    • Halgasova, N.1    Mesarosova, I.2    Bukovska, G.3
  • 47
    • 0036267740 scopus 로고    scopus 로고
    • Identification of genes that are associated with DNA repeats in prokaryotes
    • Jansen R, Embden JDA, Gaastra W, Schouls LM. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43:1565-1575.
    • (2002) Mol. Microbiol , vol.43 , pp. 1565-1575
    • Jansen, R.1    Embden, J.D.A.2    Gaastra, W.3    Schouls, L.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.