메뉴 건너뛰기




Volumn 17, Issue 10, 2007, Pages 1496-1504

The evolution of genome compression and genomic novelty in RNA viruses

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EVOLUTION; FRAMESHIFT MUTATION; GENE MUTATION; GENE STRUCTURE; GENETIC ANALYSIS; GENOME SIZE; NONHUMAN; PRIORITY JOURNAL; RNA VIRUS; VIRAL GENETICS;

EID: 34948894065     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.6305707     Document Type: Article
Times cited : (126)

References (47)
  • 1
    • 14844348002 scopus 로고    scopus 로고
    • Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein
    • doi: 10.1093/nar/gki292
    • Baril, M. and Brakier-Gingras, L. 2005. Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein. Nucleic Acids Res. 33: 1474-1486. doi: 10.1093/nar/gki292.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1474-1486
    • Baril, M.1    Brakier-Gingras, L.2
  • 2
    • 0242542705 scopus 로고    scopus 로고
    • Patterns of epistasis in RNA viruses: A review of the evidence from vaccine design
    • Burch, C.L., Turner, P.E., and Hanley, K.A. 2003. Patterns of epistasis in RNA viruses: A review of the evidence from vaccine design. J. Evol. Biol. 16: 1223-1235.
    • (2003) J. Evol. Biol , vol.16 , pp. 1223-1235
    • Burch, C.L.1    Turner, P.E.2    Hanley, K.A.3
  • 3
    • 0142088791 scopus 로고    scopus 로고
    • Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses
    • Chare, E.R., Gould, E.A., and Holmes, E.C. 2003. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 84: 2691-2703.
    • (2003) J. Gen. Virol , vol.84 , pp. 2691-2703
    • Chare, E.R.1    Gould, E.A.2    Holmes, E.C.3
  • 4
    • 33846018059 scopus 로고    scopus 로고
    • The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens
    • doi: 10.1371/journal.ppat.0020136
    • Codoñer, F.M., Daròs, J.A., Solé, R.V., and Elena, S.F. 2006. The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog. 2: e136. doi: 10.1371/journal.ppat.0020136.
    • (2006) PLoS Pathog , vol.2
    • Codoñer, F.M.1    Daròs, J.A.2    Solé, R.V.3    Elena, S.F.4
  • 5
    • 11444257029 scopus 로고    scopus 로고
    • Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution
    • Cristina, J., Lopez, F., Moratorio, G., Lopez, L., Vasquez, S., Garcia-Aguirre, L., and Chunga, A. 2005. Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution. J. Gen. Virol. 86: 115-120.
    • (2005) J. Gen. Virol , vol.86 , pp. 115-120
    • Cristina, J.1    Lopez, F.2    Moratorio, G.3    Lopez, L.4    Vasquez, S.5    Garcia-Aguirre, L.6    Chunga, A.7
  • 6
    • 0035811016 scopus 로고    scopus 로고
    • RNA virus error catastrophe: Direct molecular test by using ribavirin
    • Crotty, S., Cameron, C.E., and Andino, R. 2001. RNA virus error catastrophe: Direct molecular test by using ribavirin. Proc. Natl. Acad. Sci. 98: 6895-6900.
    • (2001) Proc. Natl. Acad. Sci , vol.98 , pp. 6895-6900
    • Crotty, S.1    Cameron, C.E.2    Andino, R.3
  • 7
    • 0033598717 scopus 로고    scopus 로고
    • Mutation rates among RNA viruses
    • Drake, J.W. and Holland, J.J. 1999. Mutation rates among RNA viruses. Proc. Natl. Acad. Sci. 96: 13910-13913.
    • (1999) Proc. Natl. Acad. Sci , vol.96 , pp. 13910-13913
    • Drake, J.W.1    Holland, J.J.2
  • 9
    • 0015133749 scopus 로고
    • Selforganization of matter and the evolution of biological macromolecules
    • Eigen, M. 1971. Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465-523.
    • (1971) Naturwissenschaften , vol.58 , pp. 465-523
    • Eigen, M.1
  • 10
    • 0031458777 scopus 로고    scopus 로고
    • Test of synergistic interactions among deleterious mutations in bacteria
    • Elena, S.F. and Lenski, R.E. 1997. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390: 395-398.
    • (1997) Nature , vol.390 , pp. 395-398
    • Elena, S.F.1    Lenski, R.E.2
  • 11
    • 33645800999 scopus 로고    scopus 로고
    • Mechanisms of genetic robustness in RNA viruses
    • Elena, S.F., Carrasco, P., Daros, J.A., and Sanjuan, R. 2006. Mechanisms of genetic robustness in RNA viruses. EMBO Rep. 7: 168-173.
    • (2006) EMBO Rep , vol.7 , pp. 168-173
    • Elena, S.F.1    Carrasco, P.2    Daros, J.A.3    Sanjuan, R.4
  • 12
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125: 1-15.
    • (1985) Am. Nat , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 13
    • 13844294363 scopus 로고    scopus 로고
    • Detecting overlapping coding sequences with pairwise alignments
    • Firth, A.E. and Brown, C.M. 2005. Detecting overlapping coding sequences with pairwise alignments. Bioinformatics 21: 282-292.
    • (2005) Bioinformatics , vol.21 , pp. 282-292
    • Firth, A.E.1    Brown, C.M.2
  • 14
    • 0033561022 scopus 로고    scopus 로고
    • Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae
    • Fukuda, Y., Washio, T., and Tomita, M. 1999. Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucleic Acids Res. 27: 1847-1853.
    • (1999) Nucleic Acids Res , vol.27 , pp. 1847-1853
    • Fukuda, Y.1    Washio, T.2    Tomita, M.3
  • 15
    • 33746099256 scopus 로고    scopus 로고
    • Recombination and the evolution of mutational robustness
    • Gardner, A. and Kalinka, A.T. 2006. Recombination and the evolution of mutational robustness. J. Theor. Biol. 241: 707-715.
    • (2006) J. Theor. Biol , vol.241 , pp. 707-715
    • Gardner, A.1    Kalinka, A.T.2
  • 16
    • 0001400708 scopus 로고
    • The effect of variation on fitness
    • Haldane, J.B.S. 1937. The effect of variation on fitness. Am. Nat. 71: 337-349.
    • (1937) Am. Nat , vol.71 , pp. 337-349
    • Haldane, J.B.S.1
  • 17
    • 0032987974 scopus 로고    scopus 로고
    • The versatility of paramyxovirus RNA polymerase stuttering
    • Hausmann, S., Garcin, D., Delenda, C., and Kolakofsky, D. 1999. The versatility of paramyxovirus RNA polymerase stuttering. J. Virol. 73: 5568-5576.
    • (1999) J. Virol , vol.73 , pp. 5568-5576
    • Hausmann, S.1    Garcin, D.2    Delenda, C.3    Kolakofsky, D.4
  • 18
    • 0345059165 scopus 로고    scopus 로고
    • Error thresholds and the constraints to RNA virus evolution
    • Holmes, E.C. 2003. Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 11: 543-546.
    • (2003) Trends Microbiol , vol.11 , pp. 543-546
    • Holmes, E.C.1
  • 19
    • 0036147047 scopus 로고    scopus 로고
    • Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
    • Jenkins, G.M., Rambaut, A., Pybus, O.G., and Holmes, E.C. 2002. Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis. J. Mol. Evol. 54: 156-165.
    • (2002) J. Mol. Evol , vol.54 , pp. 156-165
    • Jenkins, G.M.1    Rambaut, A.2    Pybus, O.G.3    Holmes, E.C.4
  • 20
    • 8744308029 scopus 로고    scopus 로고
    • Properties of overlapping genes are conserved across microbial genomes
    • Johnson, Z.I. and Chisholm, S.W. 2004. Properties of overlapping genes are conserved across microbial genomes. Genome Res. 14: 2268-2272.
    • (2004) Genome Res , vol.14 , pp. 2268-2272
    • Johnson, Z.I.1    Chisholm, S.W.2
  • 21
    • 0029992175 scopus 로고    scopus 로고
    • On the prevalence of certain codons ("RNY") in genes for proteins
    • Jukes, T.H. 1996. On the prevalence of certain codons ("RNY") in genes for proteins. J. Mol. Evol. 42: 377-381.
    • (1996) J. Mol. Evol , vol.42 , pp. 377-381
    • Jukes, T.H.1
  • 22
    • 0026722407 scopus 로고
    • Origins of genes: "Big bang" or continuous creation
    • Keese, P.K. and Gibbs, A. 1992. Origins of genes: "Big bang" or continuous creation. Proc. Natl. Acad. Sci. 89: 9489-9493.
    • (1992) Proc. Natl. Acad. Sci , vol.89 , pp. 9489-9493
    • Keese, P.K.1    Gibbs, A.2
  • 23
    • 0000977985 scopus 로고
    • The mutational load with epistatic gene interactions in fitness
    • Kimura, M. and Maruyama, T. 1966. The mutational load with epistatic gene interactions in fitness. Genetics 54: 1337-1351.
    • (1966) Genetics , vol.54 , pp. 1337-1351
    • Kimura, M.1    Maruyama, T.2
  • 24
    • 0033926304 scopus 로고    scopus 로고
    • Stability and evolution of overlapping genes
    • Krakauer, D.C. 2000. Stability and evolution of overlapping genes. Evolution 54: 731-739.
    • (2000) Evolution , vol.54 , pp. 731-739
    • Krakauer, D.C.1
  • 25
    • 0037022396 scopus 로고    scopus 로고
    • Redundancy, antiredundancy, and the robustness of genomes
    • Krakauer, D.C. and Plotkin, J.B. 2002. Redundancy, antiredundancy, and the robustness of genomes. Proc. Natl. Acad. Sci. 99: 1405-1409.
    • (2002) Proc. Natl. Acad. Sci , vol.99 , pp. 1405-1409
    • Krakauer, D.C.1    Plotkin, J.B.2
  • 26
    • 0028988480 scopus 로고
    • Identification of a Rev-related protein by analysis of spliced transcripts of the human endogenous retroviruses HTDV/HERV-K
    • Lower, R., Tonjes, R.R., Korbmacher, C., Kurth, R., and Lower, J. 1995. Identification of a Rev-related protein by analysis of spliced transcripts of the human endogenous retroviruses HTDV/HERV-K. J. Virol. 69: 141-149.
    • (1995) J. Virol , vol.69 , pp. 141-149
    • Lower, R.1    Tonjes, R.R.2    Korbmacher, C.3    Kurth, R.4    Lower, J.5
  • 27
    • 0033809519 scopus 로고    scopus 로고
    • In vivo analysis of human T-cell leukemia virus type 1 reverse transcription accuracy
    • Mansky, L.M. 2000. In vivo analysis of human T-cell leukemia virus type 1 reverse transcription accuracy. J. Virol. 74: 9525-9531.
    • (2000) J. Virol , vol.74 , pp. 9525-9531
    • Mansky, L.M.1
  • 28
    • 0031030479 scopus 로고    scopus 로고
    • Constrained evolution with respect to gene overlap of hepatitis B virus
    • Mizokami, M., Orito, E., Ohba, K., Ikeo, K., Lau, J.Y., and Gojobori, T. 1997. Constrained evolution with respect to gene overlap of hepatitis B virus. J. Mol. Evol. 44: S83-S90.
    • (1997) J. Mol. Evol , vol.44
    • Mizokami, M.1    Orito, E.2    Ohba, K.3    Ikeo, K.4    Lau, J.Y.5    Gojobori, T.6
  • 29
    • 27844567907 scopus 로고    scopus 로고
    • Evolution of mutational robustness in an RNA virus
    • doi: 10.1371/journal.pbio.0030381
    • Montville, R., Froissart, R., Remold, S.K., Tenaillon, O., and Turner, P.E. 2005. Evolution of mutational robustness in an RNA virus. PLoS Biol. 3: e381. doi: 10.1371/journal.pbio.0030381.
    • (2005) PLoS Biol , vol.3
    • Montville, R.1    Froissart, R.2    Remold, S.K.3    Tenaillon, O.4    Turner, P.E.5
  • 31
    • 0027071241 scopus 로고
    • What is a quasispecies?
    • Nowak, M.A. 1992. What is a quasispecies? Trends Ecol. Evol. 7: 118-121.
    • (1992) Trends Ecol. Evol , vol.7 , pp. 118-121
    • Nowak, M.A.1
  • 32
    • 0030976687 scopus 로고    scopus 로고
    • On the informational content of overlapping genes in prokaryotic and eukaryotic viruses
    • Pavesi, A., DeIaco, B., Granero, M.I., and Porati, A. 1997. On the informational content of overlapping genes in prokaryotic and eukaryotic viruses. J. Mol. Evol. 44: 625-631.
    • (1997) J. Mol. Evol , vol.44 , pp. 625-631
    • Pavesi, A.1    DeIaco, B.2    Granero, M.I.3    Porati, A.4
  • 35
    • 33749242962 scopus 로고    scopus 로고
    • Epistasis correlates to genomic complexity
    • Sanjuan, R. and Elena, S.F. 2006. Epistasis correlates to genomic complexity. Proc. Natl. Acad. Sci. 103: 14402-14405.
    • (2006) Proc. Natl. Acad. Sci , vol.103 , pp. 14402-14405
    • Sanjuan, R.1    Elena, S.F.2
  • 36
    • 2942565781 scopus 로고    scopus 로고
    • The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
    • Sanjuan, R., Moya, A., and Elena, S.F. 2004. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl. Acad. Sci. 101: 8396-8401.
    • (2004) Proc. Natl. Acad. Sci , vol.101 , pp. 8396-8401
    • Sanjuan, R.1    Moya, A.2    Elena, S.F.3
  • 37
    • 34347327212 scopus 로고    scopus 로고
    • Selection for robustness in mutagenized RNA viruses
    • doi: 10.1371/journal.pgen.0030093
    • Sanjuan, R., Cuevas, J.M., Furió, V., Holmes, E.C., and Moya, A. 2007. Selection for robustness in mutagenized RNA viruses. PLoS Genet. 3: e93. doi: 10.1371/journal.pgen.0030093.
    • (2007) PLoS Genet , vol.3
    • Sanjuan, R.1    Cuevas, J.M.2    Furió, V.3    Holmes, E.C.4    Moya, A.5
  • 38
    • 8144223724 scopus 로고    scopus 로고
    • The ambush hypothesis: Hidden stop codons prevent off-frame gene reading
    • Seligmann, H. and Pollock, D.D. 2004. The ambush hypothesis: Hidden stop codons prevent off-frame gene reading. DNA Cell Biol. 23: 701-705.
    • (2004) DNA Cell Biol , vol.23 , pp. 701-705
    • Seligmann, H.1    Pollock, D.D.2
  • 39
    • 12244297403 scopus 로고    scopus 로고
    • High rate of viral evolution associated with the emergence of carnivore parvovirus
    • Shackelton, L.A., Parrish, C.R., Truyen, U., and Holmes, E.C. 2005. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc. Natl. Acad. Sci. 102: 379-384.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 379-384
    • Shackelton, L.A.1    Parrish, C.R.2    Truyen, U.3    Holmes, E.C.4
  • 40
    • 0019453879 scopus 로고
    • Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code
    • Shepherd, J.C.W. 1981. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 17: 94-102.
    • (1981) J. Mol. Evol , vol.17 , pp. 94-102
    • Shepherd, J.C.W.1
  • 41
    • 0027064537 scopus 로고
    • Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase
    • Steinhauer, D.A., Domingo, E., and Holland, J.J. 1992. Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase. Gene 122: 281-288.
    • (1992) Gene , vol.122 , pp. 281-288
    • Steinhauer, D.A.1    Domingo, E.2    Holland, J.J.3
  • 42
    • 0011754335 scopus 로고
    • Transduction of a cellular oncogene - the genesis of Rous sarcoma virus
    • Swanstrom, R., Parker, R.C., Varmus, H.E., and Bishop, J.M. 1983. Transduction of a cellular oncogene - the genesis of Rous sarcoma virus. Proc. Natl. Acad. Sci. 80: 2519-2523.
    • (1983) Proc. Natl. Acad. Sci , vol.80 , pp. 2519-2523
    • Swanstrom, R.1    Parker, R.C.2    Varmus, H.E.3    Bishop, J.M.4
  • 44
    • 0035452110 scopus 로고    scopus 로고
    • Alternative definitions of epistasis: Dependence and interaction
    • Wade, M.J., Winther, R.G., Agrawal, A.F., and Goodnight, C.J. 2001. Alternative definitions of epistasis: Dependence and interaction. Trends Ecol. Evol. 16: 498-504.
    • (2001) Trends Ecol. Evol , vol.16 , pp. 498-504
    • Wade, M.J.1    Winther, R.G.2    Agrawal, A.F.3    Goodnight, C.J.4
  • 45
    • 0037469371 scopus 로고    scopus 로고
    • Evolution of mutational robustness
    • Wilke, C.O. and Adami, C. 2003. Evolution of mutational robustness. Mutat. Res. 522: 3-11.
    • (2003) Mutat. Res , vol.522 , pp. 3-11
    • Wilke, C.O.1    Adami, C.2
  • 46
    • 0035913336 scopus 로고    scopus 로고
    • Evolution of digital organisms at high mutation rates leads to survival of the flattest
    • Wilke, C.O., Wang, J.L., Ofria, C., Lenski, R.E., and Adami, C. 2001. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412: 331-333.
    • (2001) Nature , vol.412 , pp. 331-333
    • Wilke, C.O.1    Wang, J.L.2    Ofria, C.3    Lenski, R.E.4    Adami, C.5
  • 47
    • 0029840630 scopus 로고    scopus 로고
    • A reevaluation of the higher taxonomy of viruses based on RNA polymerases
    • Zanotto, P.M.D., Gibbs, M.J., Gould, E.A., and Holmes, E.C. 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol. 70: 6083-6096.
    • (1996) J. Virol , vol.70 , pp. 6083-6096
    • Zanotto, P.M.D.1    Gibbs, M.J.2    Gould, E.A.3    Holmes, E.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.