메뉴 건너뛰기




Volumn 49, Issue 2, 2007, Pages 246-254

Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L

Author keywords

Chloroplast; Codon usage; Mitochondrion; Neutral mutation; Nuclear gene; Selection constraint; Triticum aestivum

Indexed keywords

CHLOROPLAST; COMPARATIVE STUDY; CORRESPONDENCE ANALYSIS; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; MITOCHONDRION; MUTATION; NATURAL SELECTION; WHEAT;

EID: 33947634052     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2007.00404.x     Document Type: Article
Times cited : (98)

References (37)
  • 1
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi H (1994). Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy. Genetics 136, 927-935.
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 2
    • 0034823625 scopus 로고    scopus 로고
    • Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains
    • Bellgard M, Schibeci D, Trifonov E, Gojobori T (2001). Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J. Mol. Evol. 53, 465-468.
    • (2001) J. Mol. Evol. , vol.53 , pp. 465-468
    • Bellgard, M.1    Schibeci, D.2    Trifonov, E.3    Gojobori, T.4
  • 3
  • 4
    • 84993842127 scopus 로고
    • Are codon usage patterns in unicellular organisms determined by selection-mutation balance
    • Bulmer M (1988). Are codon usage patterns in unicellular organisms determined by selection-mutation balance ? J. Mol. Biol. 1, 15-26.
    • (1988) J. Mol. Biol. , vol.1 , pp. 15-26
    • Bulmer, M.1
  • 5
    • 0344653653 scopus 로고    scopus 로고
    • Codon usage and gene function are related in sequences of Arabidopsis thaliana
    • Chiapello HF, Lisacek F, Caboche M, Henaut A (1998). Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209, 1-38.
    • (1998) Gene , vol.209 , pp. 1-38
    • Chiapello, H.F.1    Lisacek, F.2    Caboche, M.3    Henaut, A.4
  • 6
    • 0027525640 scopus 로고
    • Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons
    • Fennoy SL, Bailey-Serres J (1993). Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons. Nucleic Acids Res. 21, 5294-5300.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 5294-5300
    • Fennoy, S.L.1    Bailey-Serres, J.2
  • 9
    • 0022881350 scopus 로고
    • Silent nucleotide substitution and G content of some mitochondria and bacterial genes
    • Jukes, TH, Bhushar, V (1986). Silent nucleotide substitution and G content of some mitochondria and bacterial genes. J. Mol. Evol. 24, 39-44.
    • (1986) J. Mol. Evol. , vol.24 , pp. 39-44
    • Jukes, T.H.1    Bhushar, V.2
  • 10
    • 0025742784 scopus 로고
    • Novel anticodon composition of transfer RNAs in Micrococcus luteus, a bacterium with a high genomeic G content
    • Kano A, Andachi Y, Ohama T, Osawa S (1991). Novel anticodon composition of transfer RNAs in Micrococcus luteus, a bacterium with a high genomeic G content. J. Mol. Biol. 221, 387-401.
    • (1991) J. Mol. Biol. , vol.221 , pp. 387-401
    • Kano, A.1    Andachi, Y.2    Ohama, T.3    Osawa, S.4
  • 11
    • 0346732986 scopus 로고    scopus 로고
    • Patterns of codon usage bias in three dicot and four monocot plant species
    • Kawabe A, Miyashita NT (2003). Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet. Syst. 78, 343-352.
    • (2003) Genes Genet. Syst. , vol.78 , pp. 343-352
    • Kawabe, A.1    Miyashita, N.T.2
  • 12
    • 14844331757 scopus 로고    scopus 로고
    • Inference of codon preferences in Arabidopsis thaliana
    • Kliman RM, Henry AN (2005). Inference of codon preferences in Arabidopsis thaliana. Int. J. Plant Sci. 166, 3-11.
    • (2005) Int. J. Plant Sci. , vol.166 , pp. 3-11
    • Kliman, R.M.1    Henry, A.N.2
  • 13
    • 0036221199 scopus 로고    scopus 로고
    • Codon usage by transposable elements and their host genes in five species
    • Lerat E, Capy P, Biémont C (2002). Codon usage by transposable elements and their host genes in five species. J. Mol. Evol. 54, 625-637.
    • (2002) J. Mol. Evol. , vol.54 , pp. 625-637
    • Lerat, E.1    Capy, P.2    Biémont, C.3
  • 14
    • 17044369160 scopus 로고    scopus 로고
    • Synonymous codon usage and gene function are strongly related in Oryza sativa
    • Liu Q, Dou S, Ji Z, Xue Q (2005). Synonymous codon usage and gene function are strongly related in Oryza sativa. BioSystems 80, 123-131.
    • (2005) BioSystems , vol.80 , pp. 123-131
    • Liu, Q.1    Dou, S.2    Ji, Z.3    Xue, Q.4
  • 15
    • 11044232003 scopus 로고    scopus 로고
    • Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa
    • Liu Q, Feng Y, Xue Q (2004). Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa. Mitochondrion 4, 313-320.
    • (2004) Mitochondrion , vol.4 , pp. 313-320
    • Liu, Q.1    Feng, Y.2    Xue, Q.3
  • 16
    • 2442517494 scopus 로고    scopus 로고
    • Synonymous codon usage bias in Oryza sativa
    • Liu Q, Feng Y, Zhao X, Dong H, Xue Q (2004). Synonymous codon usage bias in Oryza sativa. Plant Sci. 167, 101-105.
    • (2004) Plant Sci. , vol.167 , pp. 101-105
    • Liu, Q.1    Feng, Y.2    Zhao, X.3    Dong, H.4    Xue, Q.5
  • 17
    • 19444363142 scopus 로고    scopus 로고
    • Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species
    • Liu Q, Xue Q (2005). Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. J. Genet. 84, 55-62.
    • (2005) J. Genet. , vol.84 , pp. 55-62
    • Liu, Q.1    Xue, Q.2
  • 18
    • 0026590789 scopus 로고
    • Rates of mitochondrial DNA evolution in sharks are slow compared with mammals
    • Martin AP, Naylor GJP, Palumbi SR (1992). Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357, 153-155.
    • (1992) Nature , vol.357 , pp. 153-155
    • Martin, A.P.1    Naylor, G.J.P.2    Palumbi, S.R.3
  • 19
    • 0032169951 scopus 로고    scopus 로고
    • Divergent evolutionary constraints on mitochondrial and nuclear genomes of malaria parasites
    • McIntosh MT, Srivastava R, Vaidya AB (1998). Divergent evolutionary constraints on mitochondrial and nuclear genomes of malaria parasites. Mol. Biochem. Parasit. 95, 69-80.
    • (1998) Mol. Biochem. Parasit. , vol.95 , pp. 69-80
    • McIntosh, M.T.1    Srivastava, R.2    Vaidya, A.B.3
  • 20
    • 0031979388 scopus 로고    scopus 로고
    • Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages
    • Morton BR (1998). Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. J. Mol. Evol. 46, 449-459.
    • (1998) J. Mol. Evol. , vol.46 , pp. 449-459
    • Morton, B.R.1
  • 21
    • 0037403391 scopus 로고    scopus 로고
    • The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA
    • Morton BR (2003). The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA. J. Mol. Evol. 56, 616-629.
    • (2003) J. Mol. Evol. , vol.56 , pp. 616-629
    • Morton, B.R.1
  • 22
    • 0030825584 scopus 로고    scopus 로고
    • Codon usage tabulated from the international DNA sequence database
    • Nakamura Y, Gojobori T, Ikemura T (1997). Codon usage tabulated from the international DNA sequence database. Nucleic Acids Res. 25, 244-245.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 244-245
    • Nakamura, Y.1    Gojobori, T.2    Ikemura, T.3
  • 23
    • 0036456491 scopus 로고    scopus 로고
    • The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants
    • Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M et al. (2002). The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics 268, 434-445.
    • (2002) Mol. Genet. Genomics , vol.268 , pp. 434-445
    • Notsu, Y.1    Masood, S.2    Nishikawa, T.3    Kubo, N.4    Akiduki, G.5    Nakazono, M.6
  • 24
    • 0023956574 scopus 로고
    • Directional mutation pressure and transfer RNA in choice of the third nucleotide of synonymous two-codon sets
    • Osawa S, Ohama T, Yamao F, Muto A, Jukes TH, Ozeki H et al. (1988). Directional mutation pressure and transfer RNA in choice of the third nucleotide of synonymous two-codon sets. Proc. Natl. Acad. Sci. USA 85, 1124-1128.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 1124-1128
    • Osawa, S.1    Ohama, T.2    Yamao, F.3    Muto, A.4    Jukes, T.H.5    Ozeki, H.6
  • 25
    • 33947683578 scopus 로고    scopus 로고
    • Anlysis of Codon Usage
    • PhD thesis University of Nottingham Nottingham
    • Peden JF (1999). Anlysis of Codon Usage. PhD thesis. University of Nottingham, Nottingham.
    • (1999)
    • Peden, J.F.1
  • 26
    • 0027323771 scopus 로고
    • Molecular characterization and evolution of a duck mitochondrial genome
    • Ramirez V, Savoie P, Morais R (1993). Molecular characterization and evolution of a duck mitochondrial genome. J. Mol. Evol. 37, 296-310.
    • (1993) J. Mol. Evol. , vol.37 , pp. 296-310
    • Ramirez, V.1    Savoie, P.2    Morais, R.3
  • 27
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The european molecular biology open software suite
    • Rice P, Longden I, Bleasby A (2000). EMBOSS: The european molecular biology open software suite. Trends Genet. 16, 276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 28
    • 0024296835 scopus 로고
    • Compositional compartmentalization and compositional patterns in the nuclear genomes of plants
    • Salinas J, Matassi G, Montero LM, Bernardi G (1988). Compositional compartmentalization and compositional patterns in the nuclear genomes of plants. Nucleic Acids Res. 16, 4269-4285.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 4269-4285
    • Salinas, J.1    Matassi, G.2    Montero, L.M.3    Bernardi, G.4
  • 29
    • 0028087047 scopus 로고
    • The plant mitochondrial genome: Physical structure, information content, RNA editing, and gene migration to the nucleus
    • Schuster W, Brennicke A (1994). The plant mitochondrial genome: Physical structure, information content, RNA editing, and gene migration to the nucleus. Annu. Rev. Plant Physiol. Mol. Biol. 45, 61-78.
    • (1994) Annu. Rev. Plant Physiol. Mol. Biol. , vol.45 , pp. 61-78
    • Schuster, W.1    Brennicke, A.2
  • 30
    • 0022856787 scopus 로고
    • An evolutionary perspective on synonymous codon usage in unicellular organisms
    • Sharp PM, Li WH (1986). An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24, 28-38.
    • (1986) J. Mol. Evol. , vol.24 , pp. 28-38
    • Sharp, P.M.1    Li, W.H.2
  • 31
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp PM, Tuohy TM, Mosurski KR (1986). Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14, 5125-5143.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.2    Mosurski, K.R.3
  • 32
    • 0023652058 scopus 로고
    • Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases
    • Shields DC, Sharp PM (1987). Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res. 15, 8023-8040.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 8023-8040
    • Shields, D.C.1    Sharp, P.M.2
  • 33
    • 0023991945 scopus 로고
    • Directional mutation pressure and neutral molecular evolution
    • Sueoka N (1988). Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85, 2653-2657.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2653-2657
    • Sueoka, N.1
  • 34
    • 0028922156 scopus 로고
    • Intra-strand parity rules of DNA base composition and usage biases of synonymous codons
    • Sueoka N (1995). Intra-strand parity rules of DNA base composition and usage biases of synonymous codons. J. Mol. Evol. 40, 318-325.
    • (1995) J. Mol. Evol. , vol.40 , pp. 318-325
    • Sueoka, N.1
  • 35
    • 0033053160 scopus 로고    scopus 로고
    • Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra- strand rule of A=T and G=C
    • Sueoka N (1999). Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra- strand rule of A=T and G=C. J. Mol. Evol. 49, 49-62.
    • (1999) J. Mol. Evol. , vol.49 , pp. 49-62
    • Sueoka, N.1
  • 36
    • 0032835971 scopus 로고    scopus 로고
    • Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position
    • Sueoka N (1999). Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.
    • (1999) Gene , vol.238 , pp. 53-58
    • Sueoka, N.1
  • 37
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.