메뉴 건너뛰기




Volumn 92, Issue 8, 2005, Pages 1221-1233

Codon usage patterns distort phylogenies from or of DNA sequences

Author keywords

Arabidopsis thaliana; Ceratodon purpureus; Convergent selection; Molecular systematics; Nicotiana tabacum; Physcomitrella patens

Indexed keywords

PHYLOGENETICS;

EID: 23044465221     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.92.8.1221     Document Type: Article
Times cited : (26)

References (50)
  • 1
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • AKASHI, H. 2003. Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.
    • (2003) Genetics , vol.164 , pp. 1291-1303
    • Akashi, H.1
  • 2
    • 0039056682 scopus 로고
    • The genetics of Primula sinensis. IV. Indications as to the ontogenetic relationship of leaf and inflorescence
    • ANDERSON, E. A., AND D. DE WINTON. 1935. The genetics of Primula sinensis. IV. Indications as to the ontogenetic relationship of leaf and inflorescence. Annals of Botany 49: 671-687.
    • (1935) Annals of Botany , vol.49 , pp. 671-687
    • Anderson, E.A.1    De Winton, D.2
  • 3
    • 0029402902 scopus 로고
    • Genomic evolution drives the evolution of the translation system
    • ANDERSSON, S. G. E., AND C. G. KURLAND. 1995. Genomic evolution drives the evolution of the translation system. Biochemistry and Cell Biology 73: 775-787.
    • (1995) Biochemistry and Cell Biology , vol.73 , pp. 775-787
    • Andersson, S.G.E.1    Kurland, C.G.2
  • 4
    • 0027428828 scopus 로고
    • Silent substitutions in mammalian genomes and their evolutionary implications
    • BERNARDI, G., D. MOUCHIROUD, AND C. GAUTIER. 1993. Silent substitutions in mammalian genomes and their evolutionary implications. Journal of Molecular Evolution 37: 583-589.
    • (1993) Journal of Molecular Evolution , vol.37 , pp. 583-589
    • Bernardi, G.1    Mouchiroud, D.2    Gautier, C.3
  • 5
    • 0027213389 scopus 로고
    • The mitochondrial genome on its way to the nucleus: Different stages of gene transfer in higher plants
    • BRENNICKE, A., L. GROHMANN, R. HIESEL, V. KNOOP, AND W. SCHUSTER. 1993. The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Letters 325: 140-145.
    • (1993) FEBS Letters , vol.325 , pp. 140-145
    • Brennicke, A.1    Grohmann, L.2    Hiesel, R.3    Knoop, V.4    Schuster, W.5
  • 6
    • 0036136814 scopus 로고    scopus 로고
    • A maximum likelihood method for analyzing pseudogene evolution: Implications for silent site evolution in humans and rodents
    • BUSTAMENTE, C. D., R. NIELSEN, AND D. L. HARTL. 2002. A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution 19: 110-117.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 110-117
    • Bustamente, C.D.1    Nielsen, R.2    Hartl, D.L.3
  • 7
    • 0034117544 scopus 로고    scopus 로고
    • Two classes of genes in plants
    • CARELS, N., AND G. BERNARDI. 2000. Two classes of genes in plants. Genetics 154: 1819-1825.
    • (2000) Genetics , vol.154 , pp. 1819-1825
    • Carels, N.1    Bernardi, G.2
  • 8
    • 0344653653 scopus 로고    scopus 로고
    • Codon usage and gene function are related in sequences of Arabidopsis thaliana
    • CHIAPELLO, H., F. LISACEK, M. CABOCHE, AND A. HÉNAUT. 1998. Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209: gc1-gc38.
    • (1998) Gene , vol.209
    • Chiapello, H.1    Lisacek, F.2    Caboche, M.3    Hénaut, A.4
  • 9
    • 0031050445 scopus 로고    scopus 로고
    • Yeast-enhanced green fluorescent protein (yEGFP): A reporter of gene expression in Candida albicans
    • CORMACK, B. P., G. BERTRAM, M. EDGERTON, N. A. GOW, S. FALKOW, AND A. S. BROWN. 1997. Yeast-enhanced green fluorescent protein (yEGFP): a reporter of gene expression in Candida albicans. Microbiology 143: 303-311.
    • (1997) Microbiology , vol.143 , pp. 303-311
    • Cormack, B.P.1    Bertram, G.2    Edgerton, M.3    Gow, N.A.4    Falkow, S.5    Brown, A.S.6
  • 10
    • 0026673926 scopus 로고
    • Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: Evidence for RNA-mediated gene transfer
    • COVELLO, P. S., AND M. W. GRAY. 1992. Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: evidence for RNA-mediated gene transfer. EMBO Journal 11: 3815-3820.
    • (1992) EMBO Journal , vol.11 , pp. 3815-3820
    • Covello, P.S.1    Gray, M.W.2
  • 11
    • 33749733044 scopus 로고
    • Chimera formation in mutagen-treated seed and diplontic selection
    • Pergamon Press, London, UK
    • D'AMATO, F. 1965. Chimera formation in mutagen-treated seed and diplontic selection. In The use of induced mutations in plant breeding, 303-315. Pergamon Press, London, UK.
    • (1965) The Use of Induced Mutations in Plant Breeding , pp. 303-315
    • D'Amato, F.1
  • 13
    • 0141935419 scopus 로고    scopus 로고
    • Mendelian controversies: A botanical and historical review
    • FAIRBANKS, D. J., AND B. RYTTING. 2001. Mendelian controversies: a botanical and historical review. American Journal of Botany 88: 737-752.
    • (2001) American Journal of Botany , vol.88 , pp. 737-752
    • Fairbanks, D.J.1    Rytting, B.2
  • 15
    • 0027525640 scopus 로고
    • Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C- and G-ending codons
    • FENNOY, S. L., AND J. BAILEY-SERRES. 1993. Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C- and G-ending codons. Nucleic Acids Research 21: 5294-5300.
    • (1993) Nucleic Acids Research , vol.21 , pp. 5294-5300
    • Fennoy, S.L.1    Bailey-Serres, J.2
  • 17
    • 0004039907 scopus 로고    scopus 로고
    • Sinauer Associates, Inc., Sunderland, Massachusetts, USA
    • FUTUYMA, D. J. 1998. Evolutionary biology, 3rd ed. Sinauer Associates, Inc., Sunderland, Massachusetts, USA.
    • (1998) Evolutionary Biology, 3rd Ed.
    • Futuyma, D.J.1
  • 18
    • 0003882082 scopus 로고
    • Oxford University Press, New York, New York, USA
    • GILLHAM, N. W. 1994. Organelle genes and genomes. Oxford University Press, New York, New York, USA.
    • (1994) Organelle Genes and Genomes
    • Gillham, N.W.1
  • 20
    • 0027978722 scopus 로고
    • Selection intensity for codon bias
    • HARTL, D. L., E. N. MORIYAMA, AND S. A. SAWYER. 1994. Selection intensity for codon bias. Genetics 138: 227-234.
    • (1994) Genetics , vol.138 , pp. 227-234
    • Hartl, D.L.1    Moriyama, E.N.2    Sawyer, S.A.3
  • 21
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular organisms
    • IKEMURA, T. 1985. Codon usage and tRNA content in unicellular organisms. Molecular Biology and Evolution 2: 13-34.
    • (1985) Molecular Biology and Evolution , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 22
    • 0029822746 scopus 로고    scopus 로고
    • Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals
    • KADOWAKI, K., N. KUBO, K. OZAWA, AND A. HIRAI. 1996. Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals. EMBO Journal 15: 6652-6661.
    • (1996) EMBO Journal , vol.15 , pp. 6652-6661
    • Kadowaki, K.1    Kubo, N.2    Ozawa, K.3    Hirai, A.4
  • 23
    • 0030946680 scopus 로고    scopus 로고
    • The structure and function of RuBisCO and their implications for systematic studies
    • KELLOGG, E. A., AND N. D. JULIANO. 1997. The structure and function of RuBisCO and their implications for systematic studies. American Journal of Botany 84: 413-428.
    • (1997) American Journal of Botany , vol.84 , pp. 413-428
    • Kellogg, E.A.1    Juliano, N.D.2
  • 24
    • 0029046676 scopus 로고
    • Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum
    • KOLUKISAOGLU, H. Ü., S. MARX, C. WIEGMANN, S. HANELT, AND H. A. W. SCHNEIDER-POETSCH. 1995. Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum. Journal of Molecular Evolution 41: 329-337.
    • (1995) Journal of Molecular Evolution , vol.41 , pp. 329-337
    • Kolukisaoglu, H.Ü.1    Marx, S.2    Wiegmann, C.3    Hanelt, S.4    Schneider-Poetsch, H.A.W.5
  • 26
    • 0028222134 scopus 로고
    • Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene
    • KWIATOWSKI, J., D. SKARECKY, K. BAILEY, AND F. J. AYALA. 1994. Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene. Journal of Molecular Evolution 38: 443-454.
    • (1994) Journal of Molecular Evolution , vol.38 , pp. 443-454
    • Kwiatowski, J.1    Skarecky, D.2    Bailey, K.3    Ayala, F.J.4
  • 27
    • 0036950836 scopus 로고    scopus 로고
    • Relationships among seed plants inferred from highly conserved genes: Sorting conflicting phylogenetic signals among ancient lineages
    • MAGALLÓN, S., AND M. J. SANDERSON. 2002. Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages. American Journal of Botany 89: 1991-2006.
    • (2002) American Journal of Botany , vol.89 , pp. 1991-2006
    • Magallón, S.1    Sanderson, M.J.2
  • 30
    • 0030934591 scopus 로고    scopus 로고
    • Rates of synonymous substitution do not indicate selective constraints on the codon use of the plant psbA gene
    • MORTON, B. R. 1997. Rates of synonymous substitution do not indicate selective constraints on the codon use of the plant psbA gene. Molecular and Biological Evolution 14: 412-419.
    • (1997) Molecular and Biological Evolution , vol.14 , pp. 412-419
    • Morton, B.R.1
  • 31
    • 0030803755 scopus 로고    scopus 로고
    • The atypical codon usage of the plant psbA gene may be the remnant of an ancestral bias
    • MORTON, B. R., AND J. A. LEVIN. 1997. The atypical codon usage of the plant psbA gene may be the remnant of an ancestral bias. Proceedings of the National Academy of Sciences, USA 94: 11434-11438.
    • (1997) Proceedings of the National Academy of Sciences, USA , vol.94 , pp. 11434-11438
    • Morton, B.R.1    Levin, J.A.2
  • 33
    • 0030054305 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates
    • MUSE, S. V. 1996. Estimating synonymous and nonsynonymous substitution rates. Molecular Biology and Evolution 13: 105-114.
    • (1996) Molecular Biology and Evolution , vol.13 , pp. 105-114
    • Muse, S.V.1
  • 34
    • 0020665560 scopus 로고
    • Frequency of spontaneous and induced "point" mutations in higher eukaryotes
    • NEEL, J. V. 1983. Frequency of spontaneous and induced "point" mutations in higher eukaryotes. Journal of Heredity 74: 2-15.
    • (1983) Journal of Heredity , vol.74 , pp. 2-15
    • Neel, J.V.1
  • 35
    • 0026091126 scopus 로고
    • RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution
    • NUGENT, J. M., AND J. D. PALMER. 1991. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66: 473-481.
    • (1991) Cell , vol.66 , pp. 473-481
    • Nugent, J.M.1    Palmer, J.D.2
  • 36
    • 0031127382 scopus 로고    scopus 로고
    • Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage
    • ROUWENDAL, G. J., O. MENDES, E. J. WOLBERT, AND A. DOUWE DE BOER. 1997. Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage. Plant Molecular Biology 33: 989-999.
    • (1997) Plant Molecular Biology , vol.33 , pp. 989-999
    • Rouwendal, G.J.1    Mendes, O.2    Wolbert, E.J.3    Douwe De Boer, A.4
  • 39
    • 0024967181 scopus 로고
    • Codon usage and gene expression level in Dictyosteluim discoideum: Highly expressed genes do 'prefer' optimal codons
    • SHARP, P. M., AND K. M. DEVINE. 1989. Codon usage and gene expression level in Dictyosteluim discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Research 17: 5029-5039.
    • (1989) Nucleic Acids Research , vol.17 , pp. 5029-5039
    • Sharp, P.M.1    Devine, K.M.2
  • 40
    • 0022856787 scopus 로고
    • An evolutionary perspective on synonymous codon usage in unicellular organisms
    • SHARP, P. M., AND W.-H. LI. 1986. An evolutionary perspective on synonymous codon usage in unicellular organisms. Journal of Molecular Evolution 24: 28-38.
    • (1986) Journal of Molecular Evolution , vol.24 , pp. 28-38
    • Sharp, P.M.1    Li, W.-H.2
  • 44
    • 0009005623 scopus 로고
    • Edward Moxon, London, UK
    • TENNYSON, A., LORD. 1850. In memoriam. Edward Moxon, London, UK.
    • (1850) In Memoriam
    • Tennyson, A.L.1
  • 45
    • 0027022238 scopus 로고
    • Molecular cloning of a novel phytochrome gene of the moss Ceratodon purpureus which encodes a putative light-regulated protein kinase
    • THÜMMLER, F., M. DUFNER, P. KREISEL, AND P. DITTRICH. 1992. Molecular cloning of a novel phytochrome gene of the moss Ceratodon purpureus which encodes a putative light-regulated protein kinase. Plant Molecular Biology 20: 1003-1017.
    • (1992) Plant Molecular Biology , vol.20 , pp. 1003-1017
    • Thümmler, F.1    Dufner, M.2    Kreisel, P.3    Dittrich, P.4
  • 46
    • 0036100820 scopus 로고    scopus 로고
    • Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis
    • TIFFIN, P., AND M. W. HAHN. 2002. Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis. Journal of Molecular Evolution 54: 746-753.
    • (2002) Journal of Molecular Evolution , vol.54 , pp. 746-753
    • Tiffin, P.1    Hahn, M.W.2
  • 47
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • WRIGHT, F. 1990. The 'effective number of codons' used in a gene. Gene 87: 23-29.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 48
    • 0029970817 scopus 로고    scopus 로고
    • Maximizing transcription efficiency causes codon usage bias
    • XIA, X. 1996. Maximizing transcription efficiency causes codon usage bias. Genetics 144: 1309-1320.
    • (1996) Genetics , vol.144 , pp. 1309-1320
    • Xia, X.1
  • 49
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • YANG, Z., AND R. NIELSEN. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19: 908-917.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 50
    • 0029909407 scopus 로고    scopus 로고
    • Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein
    • YUANG, T. T., L. CHENG, AND S. R. KAIN. 1996. Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. Nucleic Acids Research 24: 4592-4593.
    • (1996) Nucleic Acids Research , vol.24 , pp. 4592-4593
    • Yuang, T.T.1    Cheng, L.2    Kain, S.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.