메뉴 건너뛰기




Volumn 6, Issue 1, 2018, Pages

The genomic underpinnings of eukaryotic virus taxonomy: Creating a sequence-based framework for family-level virus classification

Author keywords

Baltimore classification; Hidden Markov model; Metagenomic; Taxon; Taxonomy; Virus; Virus classification

Indexed keywords

ARTICLE; BOOTSTRAPPING; EUKARYOTE; GENE SEQUENCE; GENE TRANSFER; GENOME SIZE; HIDDEN MARKOV MODEL; MARYLAND; METAGENOMICS; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; TAXONOMY; VALIDATION PROCESS; VIRUS CLASSIFICATION; VIRUS GENE; CLASSIFICATION; GENETICS; HOST RANGE; MOLECULAR EVOLUTION; VIROLOGY; VIRUS; VIRUS GENOME;

EID: 85042872875     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/s40168-018-0422-7     Document Type: Article
Times cited : (70)

References (57)
  • 1
    • 84947549860 scopus 로고    scopus 로고
    • The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus
    • Abergel C, Legendre M, Claverie JM. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. FEMS Microbiol Rev. 2015;39:779-96
    • (2015) FEMS Microbiol Rev , vol.39 , pp. 779-796
    • Abergel, C.1    Legendre, M.2    Claverie, J.M.3
  • 2
    • 0015114139 scopus 로고
    • Expression of animal virus genomes
    • Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971;35:235-41
    • (1971) Bacteriol Rev , vol.35 , pp. 235-241
    • Baltimore, D.1
  • 4
    • 84857371051 scopus 로고    scopus 로고
    • Metagenomics and future perspectives in virus discovery
    • Mokili JL, Rohwer F, Dutilh BE. Metagenomics and future perspectives in virus discovery. Curr Opin Virol. 2012;2:63-77
    • (2012) Curr Opin Virol , vol.2 , pp. 63-77
    • Mokili, J.L.1    Rohwer, F.2    Dutilh, B.E.3
  • 5
    • 80053370586 scopus 로고    scopus 로고
    • Exploring the viral world through metagenomics
    • Rosario K, Breitbart M. Exploring the viral world through metagenomics. Curr Opin Virol. 2011;1:289-97
    • (2011) Curr Opin Virol , vol.1 , pp. 289-297
    • Rosario, K.1    Breitbart, M.2
  • 6
    • 84969131071 scopus 로고    scopus 로고
    • Biogeography of viruses in the sea
    • Chow CE, Suttle CA. Biogeography of viruses in the sea. Annu Rev Virol. 2015;2:41-66
    • (2015) Annu Rev Virol , vol.2 , pp. 41-66
    • Chow, C.E.1    Suttle, C.A.2
  • 10
    • 77953692396 scopus 로고    scopus 로고
    • Origin and evolution of eukaryotic large nucleocytoplasmic DNA viruses
    • Koonin EV, Yutin N. Origin and evolution of eukaryotic large nucleocytoplasmic DNA viruses. Intervirology. 2010;53:284-92
    • (2010) Intervirology , vol.53 , pp. 284-292
    • Koonin, E.V.1    Yutin, N.2
  • 14
    • 85017009622 scopus 로고    scopus 로고
    • Polydnaviruses: nature's genetic engineers
    • Strand MR, Burke GR. Polydnaviruses: nature's genetic engineers. Annu Rev Virol. 2014;1:333-54
    • (2014) Annu Rev Virol , vol.1 , pp. 333-354
    • Strand, M.R.1    Burke, G.R.2
  • 15
    • 0030812842 scopus 로고    scopus 로고
    • Homologous sequences in the Campoletis sonorensis polydnavirus genome are implicated in replication and nesting of the W segment family
    • Cui L, Webb BA. Homologous sequences in the Campoletis sonorensis polydnavirus genome are implicated in replication and nesting of the W segment family. J Virol. 1997;71:8504-13
    • (1997) J Virol , vol.71 , pp. 8504-8513
    • Cui, L.1    Webb, B.A.2
  • 18
    • 0023098848 scopus 로고
    • Structural and functional homology of parvovirus and papovavirus polypeptides
    • Astell CR, Mol CD, Anderson WF. Structural and functional homology of parvovirus and papovavirus polypeptides. J Gen Virol. 1987;68(Pt 3):885-93
    • (1987) J Gen Virol , vol.68 , pp. 885-893
    • Astell, C.R.1    Mol, C.D.2    Anderson, W.F.3
  • 19
    • 0030820351 scopus 로고    scopus 로고
    • Bovine papillomavirus type 1 E1 and simian virus 40 large T antigen share regions of sequence similarity required for multiple functions
    • Mansky KC, Batiza A, Lambert PF. Bovine papillomavirus type 1 E1 and simian virus 40 large T antigen share regions of sequence similarity required for multiple functions. J Virol. 1997;71:7600-8
    • (1997) J Virol , vol.71 , pp. 7600-7608
    • Mansky, K.C.1    Batiza, A.2    Lambert, P.F.3
  • 20
    • 85012164580 scopus 로고    scopus 로고
    • Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae
    • Varsani A, Krupovic M. Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evol. 2017;3:vew037
    • (2017) Virus Evol , vol.3
    • Varsani, A.1    Krupovic, M.2
  • 22
    • 0026655694 scopus 로고
    • Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: delineation of an additional group of positive-strand RNA plant and animal viruses
    • Koonin EV, Gorbalenya AE, Purdy MA, Rozanov MN, Reyes GR, Bradley DW. Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: delineation of an additional group of positive-strand RNA plant and animal viruses. ProcNatlAcadSciUSA. 1992;89:8259-63
    • (1992) ProcNatlAcadSciUSA , vol.89 , pp. 8259-8263
    • Koonin, E.V.1    Gorbalenya, A.E.2    Purdy, M.A.3    Rozanov, M.N.4    Reyes, G.R.5    Bradley, D.W.6
  • 23
    • 84938871300 scopus 로고    scopus 로고
    • Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins
    • Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol. 2015;6:696
    • (2015) Front Microbiol , vol.6 , pp. 696
    • Rosario, K.1    Schenck, R.O.2    Harbeitner, R.C.3    Lawler, S.N.4    Breitbart, M.5
  • 25
    • 84995699235 scopus 로고    scopus 로고
    • Novel circular single-stranded DNA viruses among an asteroid, echinoid and Holothurian (phylum: Echinodermata)
    • Jackson EW, Bistolas KS, Button JB, Hewson I. Novel circular single-stranded DNA viruses among an asteroid, echinoid and Holothurian (phylum: Echinodermata). PLoS One. 2016;11:e0166093
    • (2016) PLoS One , vol.11
    • Jackson, E.W.1    Bistolas, K.S.2    Button, J.B.3    Hewson, I.4
  • 26
    • 84892988070 scopus 로고    scopus 로고
    • Comparative metagenomics: natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences
    • McDaniel LD, Rosario K, Breitbart M, Paul JH. Comparative metagenomics: natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences. Environ Microbiol. 2014;16:570-85
    • (2014) Environ Microbiol , vol.16 , pp. 570-585
    • McDaniel, L.D.1    Rosario, K.2    Breitbart, M.3    Paul, J.H.4
  • 28
    • 84954108374 scopus 로고    scopus 로고
    • Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses
    • Shi M, Lin XD, Vasilakis N, Tian JH, Li CX, Chen LJ, Eastwood G, Diao XN, Chen MH, Chen X, et al. Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. J Virol. 2015;90:659-69
    • (2015) J Virol , vol.90 , pp. 659-669
    • Shi, M.1    Lin, X.D.2    Vasilakis, N.3    Tian, J.H.4    Li, C.X.5    Chen, L.J.6    Eastwood, G.7    Diao, X.N.8    Chen, M.H.9    Chen, X.10
  • 29
    • 84958697849 scopus 로고    scopus 로고
    • Network-thinking: graphs to analyze microbial complexity and evolution
    • Corel E, Lopez P, Meheust R, Bapteste E. Network-thinking: graphs to analyze microbial complexity and evolution. Trends Microbiol. 2016;24:224-37
    • (2016) Trends Microbiol , vol.24 , pp. 224-237
    • Corel, E.1    Lopez, P.2    Meheust, R.3    Bapteste, E.4
  • 31
    • 84986587931 scopus 로고    scopus 로고
    • The double-stranded DNA virosphere as a modular hierarchical network of gene sharing
    • Iranzo J, Krupovic M, Koonin EV: The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. MBio. 2016;7:e00978-16
    • (2016) MBio , vol.7
    • Iranzo, J.1    Krupovic, M.2    Koonin, E.V.3
  • 32
    • 85018974675 scopus 로고    scopus 로고
    • vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and bacteria
    • Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and bacteria. PeerJ. 2017;5:e3243
    • (2017) PeerJ , vol.5
    • Bolduc, B.1    Jang, H.B.2    Doulcier, G.3    You, Z.Q.4    Roux, S.5    Sullivan, M.B.6
  • 33
    • 79956105255 scopus 로고    scopus 로고
    • What does virus evolution tell us about virus origins?
    • Holmes EC. What does virus evolution tell us about virus origins? J Virol. 2011;85:5247-51
    • (2011) J Virol , vol.85 , pp. 5247-5251
    • Holmes, E.C.1
  • 35
    • 0027769867 scopus 로고
    • Progress towards a higher taxonomy of viruses
    • Ward CW. Progress towards a higher taxonomy of viruses. Res Virol. 1993;144:419-53
    • (1993) Res Virol , vol.144 , pp. 419-453
    • Ward, C.W.1
  • 36
    • 84923073842 scopus 로고    scopus 로고
    • Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases
    • Monttinen HA, Ravantti JJ, Stuart DI, Poranen MM. Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases. Mol Biol Evol. 2014;31:2741-52
    • (2014) Mol Biol Evol , vol.31 , pp. 2741-2752
    • Monttinen, H.A.1    Ravantti, J.J.2    Stuart, D.I.3    Poranen, M.M.4
  • 37
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005;21:951-60
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 38
    • 70549108054 scopus 로고    scopus 로고
    • Hidden Markov models and their applications in biological sequence analysis
    • Yoon BJ. Hidden Markov models and their applications in biological sequence analysis. Curr Genomics. 2009;10:402-15
    • (2009) Curr Genomics , vol.10 , pp. 402-415
    • Yoon, B.J.1
  • 39
    • 19844377248 scopus 로고    scopus 로고
    • Recent applications of hidden Markov models in computational biology
    • Choo KH, Tong JC, Zhang L. Recent applications of hidden Markov models in computational biology. Genomics Proteomics Bioinformatics. 2004;2:84-96
    • (2004) Genomics Proteomics Bioinformatics , vol.2 , pp. 84-96
    • Choo, K.H.1    Tong, J.C.2    Zhang, L.3
  • 40
    • 0035082495 scopus 로고    scopus 로고
    • Identification of related proteins with weak sequence identity using secondary structure information
    • Geourjon C, Combet C, Blanchet C, Deleage G. Identification of related proteins with weak sequence identity using secondary structure information. Protein Sci. 2001;10:788-97
    • (2001) Protein Sci , vol.10 , pp. 788-797
    • Geourjon, C.1    Combet, C.2    Blanchet, C.3    Deleage, G.4
  • 41
    • 70149097323 scopus 로고    scopus 로고
    • An introduction to sequence similarity ("homology") searching
    • Chapter 3:Unit 3.1:3.1.1-7
    • Stormo GD. An introduction to sequence similarity ("homology") searching. Curr Protoc Bioinformatics. 2009;27:Chapter 3:Unit 3.1:3.1.1-7
    • (2009) Curr Protoc Bioinformatics , vol.27
    • Stormo, G.D.1
  • 42
    • 77954196482 scopus 로고    scopus 로고
    • Low-homology protein threading
    • Peng J, Xu J. Low-homology protein threading. Bioinformatics. 2010;26:i294-300
    • (2010) Bioinformatics , vol.26
    • Peng, J.1    Xu, J.2
  • 43
    • 0033578669 scopus 로고    scopus 로고
    • Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures
    • Benson SD, Bamford JK, Bamford DH, Burnett RM. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell. 1999;98:825-33
    • (1999) Cell , vol.98 , pp. 825-833
    • Benson, S.D.1    Bamford, J.K.2    Bamford, D.H.3    Burnett, R.M.4
  • 44
    • 84898995103 scopus 로고    scopus 로고
    • Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages
    • Rixon FJ, Schmid MF. Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages. Curr Opin Virol. 2014;5:105-10
    • (2014) Curr Opin Virol , vol.5 , pp. 105-110
    • Rixon, F.J.1    Schmid, M.F.2
  • 45
    • 20444449200 scopus 로고    scopus 로고
    • The limits of protein sequence comparison?
    • Pearson WR, Sierk ML. The limits of protein sequence comparison? Curr Opin Struct Biol. 2005;15:254-60
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 254-260
    • Pearson, W.R.1    Sierk, M.L.2
  • 46
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999;12:85-94
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 47
    • 85016571844 scopus 로고    scopus 로고
    • Nucleic and amino acid sequences support structure-based viral classification
    • Sinclair RM, Ravantti JJ, Bamford DH: Nucleic and amino acid sequences support structure-based viral classification. J Virol. 2017;91:e02275-16
    • (2017) J Virol , vol.91
    • Sinclair, R.M.1    Ravantti, J.J.2    Bamford, D.H.3
  • 48
    • 85031780472 scopus 로고    scopus 로고
    • Sequence analysis of malacoherpesvirus proteins: pan-herpesvirus capsid module and replication enzymes with an ancient connection to "Megavirales"
    • Mushegian A, Karin EL, Pupko T. Sequence analysis of malacoherpesvirus proteins: pan-herpesvirus capsid module and replication enzymes with an ancient connection to "Megavirales". Virology. 2017;513:114-28
    • (2017) Virology , vol.513 , pp. 114-128
    • Mushegian, A.1    Karin, E.L.2    Pupko, T.3
  • 49
    • 68149150518 scopus 로고    scopus 로고
    • Symbiotic virus at the evolutionary intersection of three types of large DNA viruses; iridoviruses, ascoviruses, and ichnoviruses
    • Bigot Y, Renault S, Nicolas J, Moundras C, Demattei MV, Samain S, Bideshi DK, Federici BA. Symbiotic virus at the evolutionary intersection of three types of large DNA viruses; iridoviruses, ascoviruses, and ichnoviruses. PLoS One. 2009;4:e6397
    • (2009) PLoS One , vol.4
    • Bigot, Y.1    Renault, S.2    Nicolas, J.3    Moundras, C.4    Demattei, M.V.5    Samain, S.6    Bideshi, D.K.7    Federici, B.A.8
  • 52
    • 61849113253 scopus 로고    scopus 로고
    • Graph clustering via a discrete uncoupling process
    • van Dongen S. Graph clustering via a discrete uncoupling process. SIAM J Matrix Anal Appl. 2008;30:121-41
    • (2008) SIAM J Matrix Anal Appl , vol.30 , pp. 121-141
    • van Dongen, S.1
  • 53
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-7
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 54
    • 50849124115 scopus 로고    scopus 로고
    • Measuring and testing dependence by correlation of distances
    • Gabor J, Székely M, Rizzo L, Bakorov NK. Measuring and testing dependence by correlation of distances. Ann Stat. 2007;35:2769-94
    • (2007) Ann Stat , vol.35 , pp. 2769-2794
    • Gabor, J.1    Székely, M.2    Rizzo, L.3    Bakorov, N.K.4
  • 55
    • 0002471149 scopus 로고
    • The comparison of dendrograms by objective methods
    • Sokall RR, Rohlf FJ. The comparison of dendrograms by objective methods. Taxon. 1962;11:33-40
    • (1962) Taxon , vol.11 , pp. 33-40
    • Sokall, R.R.1    Rohlf, F.J.2
  • 56
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: a python library for phylogenetic computing
    • Sukumaran J, Holder MT. DendroPy: a python library for phylogenetic computing. Bioinformatics. 2010;26:1569-71
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.