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Volumn 52, Issue 12, 2010, Pages 1100-1108

Complex Mutation and Weak Selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE; TRANSFER RNA;

EID: 78649568720     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2010.00998.x     Document Type: Article
Times cited : (10)

References (34)
  • 1
    • 0035546157 scopus 로고    scopus 로고
    • Gene expression and molecular evolution
    • Akashi H (2001) Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11, 660-666.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 660-666
    • Akashi, H.1
  • 2
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer M (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129, 897-907.
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 3
    • 0344653653 scopus 로고    scopus 로고
    • Codon usage and gene function are related in sequences of Arabidopsis thaliana
    • Chiapello H, 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.1    Lisacek, F.2    Caboche, M.3    Henaut, A.4
  • 4
    • 0036889468 scopus 로고    scopus 로고
    • Evolution of synonymous codon usage in metazoans
    • Duret L (2002) Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12, 640-649.
    • (2002) Curr. Opin. Genet. Dev. , vol.12 , pp. 640-649
    • Duret, L.1
  • 5
    • 40649096810 scopus 로고    scopus 로고
    • Impact of bias discrepancy and amino acid usage on estimates of the effective number of codon used in a gene, and a test for selection on codon usage
    • Fuglsang A (2008) Impact of bias discrepancy and amino acid usage on estimates of the effective number of codon used in a gene, and a test for selection on codon usage. Gene 410, 82-88.
    • (2008) Gene , vol.410 , pp. 82-88
    • Fuglsang, A.1
  • 6
    • 0033525788 scopus 로고    scopus 로고
    • Mitochondrial evolution
    • Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283, 1476-1481.
    • (1999) Science , vol.283 , pp. 1476-1481
    • Gray, M.W.1    Burger, G.2    Lang, B.F.3
  • 7
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optical for the E. coli translational system
    • Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optical for the E. coli translational system. J. Mol. Biol. 151, 389-409.
    • (1981) J. Mol. Biol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 8
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2, 13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 9
    • 33847686233 scopus 로고    scopus 로고
    • Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula
    • Ingvarsson PK (2007) Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol. Biol. Evol. 24, 836-844.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 836-844
    • Ingvarsson, P.K.1
  • 10
    • 38949118287 scopus 로고    scopus 로고
    • Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection
    • Jia WL, Higgs PG (2007) Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol. Biol. Evol. 25, 339-351.
    • (2007) Mol. Biol. Evol. , vol.25 , pp. 339-351
    • Jia, W.L.1    Higgs, P.G.2
  • 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 preference in Arabidopsis thaliana
    • Kliman RM, Henry AN (2005) Inference of codon preference in Arabidopsis thaliana. J. Plant Sci. 166, 3-11.
    • (2005) J. Plant Sci. , vol.166 , pp. 3-11
    • Kliman, R.M.1    Henry, A.N.2
  • 13
    • 67349286953 scopus 로고    scopus 로고
    • The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes
    • Li L, Wang B, Liu Y, Qiu YL (2009) The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J. Mol. Evol. 68, 665-678.
    • (2009) J. Mol. Evol. , vol.68 , pp. 665-678
    • Li, L.1    Wang, B.2    Liu, Y.3    Qiu, Y.L.4
  • 14
    • 11044232003 scopus 로고    scopus 로고
    • Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa
    • Liu QP, Feng Y, Xue QZ (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.P.1    Feng, Y.2    Xue, Q.Z.3
  • 15
    • 0013596021 scopus 로고
    • The guanine and cytosine content of genomic DNA and bacterial evolution
    • Muto A, Osawa S (1987) The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84, 166-169.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 166-169
    • Muto, A.1    Osawa, S.2
  • 16
    • 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
  • 17
    • 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
  • 18
    • 0030803755 scopus 로고    scopus 로고
    • The atypical codon usage of the plant psbA gene may be the remnant of an ancestral bias
    • Morton BR, Levin JA (1997) The atypical codon usage of the plant psbA gene may be the remnant of an ancestral bias. Proc. Natl. Acad. Sci. USA 94, 11434-11438.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11434-11438
    • Morton, B.R.1    Levin, J.A.2
  • 19
    • 33845873056 scopus 로고    scopus 로고
    • Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana
    • Morton BR, Wright SI (2007) Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana. Mol. Biol. Evol. 24, 122-129.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 122-129
    • Morton, B.R.1    Wright, S.I.2
  • 20
    • 0026558482 scopus 로고
    • Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA - A primitive form of plant mitochondrial genome
    • Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA - A primitive form of plant mitochondrial genome. J. Mol. Biol. 223, 1-7.
    • (1992) J. Mol. Biol. , vol.223 , pp. 1-7
    • Oda, K.1    Yamato, K.2    Ohta, E.3    Nakamura, Y.4    Takemura, M.5    Nozato, N.6    Akashi, K.7    Kanegae, T.8    Ogura, Y.9    Kohchi, T.10    Ohyama, K.11
  • 21
    • 0025283965 scopus 로고
    • Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content
    • Ohama T, Muto A, Osawa S (1990) Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content. Nucl. Acids Res. 18, 1565-1569.
    • (1990) Nucl. Acids Res. , vol.18 , pp. 1565-1569
    • Ohama, T.1    Muto, A.2    Osawa, S.3
  • 22
    • 78649599866 scopus 로고    scopus 로고
    • () Analysis of Codon Usages., PhD Thesis, University of Nottingham
    • Pedan JF (2000) Analysis of Codon Usages. PhD Thesis University of Nottingham
    • (2000)
    • Pedan, J.F.1
  • 25
    • 8744310123 scopus 로고    scopus 로고
    • Codon usage bias from tRNA's point of view: redundancy, specialization, and decoding for translation optimization
    • Rocha EPC (2004) Codon usage bias from tRNA's point of view: redundancy, specialization, and decoding for translation optimization. Genome Res. 14, 2279-2286.
    • (2004) Genome Res. , vol.14 , pp. 2279-2286
    • Rocha, E.P.C.1
  • 26
    • 27744507140 scopus 로고    scopus 로고
    • A problem in multivariate analysis of codon usage data and a possible solution
    • Suzuki H, Saito R, Tomita M (2005) A problem in multivariate analysis of codon usage data and a possible solution. FEBS Lett. 579, 6499-6504.
    • (2005) FEBS Lett. , vol.579 , pp. 6499-6504
    • Suzuki, H.1    Saito, R.2    Tomita, M.3
  • 27
    • 33847669179 scopus 로고    scopus 로고
    • The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants
    • Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N (2007) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol. Biol. Evol. 24, 699-709.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 699-709
    • Terasawa, K.1    Odahara, M.2    Kabeya, Y.3    Kikugawa, T.4    Sekine, Y.5    Fujiwara, M.6    Sato, N.7
  • 28
    • 71149092653 scopus 로고    scopus 로고
    • The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts
    • Wang B, Xue J, Li L, Liu Y, Qiu YL (2009) The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr. Genet. 55, 601-611.
    • (2009) Curr. Genet. , vol.55 , pp. 601-611
    • Wang, B.1    Xue, J.2    Li, L.3    Liu, Y.4    Qiu, Y.L.5
  • 29
    • 33746685034 scopus 로고    scopus 로고
    • Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants
    • Wang L, Roossinck MJ (2006) Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants. Plant Mol. Biol. 61, 699-710.
    • (2006) Plant Mol. Biol. , vol.61 , pp. 699-710
    • Wang, L.1    Roossinck, M.J.2
  • 30
    • 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
  • 31
    • 4143122090 scopus 로고    scopus 로고
    • Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
    • Wright SI, Kenneth Yau CB, Looseley M, Meyers BC (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol. Biol. Evol. 21, 1719-1726.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1719-1726
    • Wright, S.I.1    Kenneth Yau, C.B.2    Looseley, M.3    Meyers, B.C.4
  • 32
    • 75049083803 scopus 로고    scopus 로고
    • The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts
    • Xue JY, Liu Y, Li L, Wang B, Qiu YL (2010) The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr. Genet. 56, 53-61.
    • (2010) Curr. Genet. , vol.56 , pp. 53-61
    • Xue, J.Y.1    Liu, Y.2    Li, L.3    Wang, B.4    Qiu, Y.L.5
  • 33
    • 33947634052 scopus 로고    scopus 로고
    • Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L
    • Zhang WJ, Zhou J, Li ZF, Wang L, Gu X, Zhong Y (2007) Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. J. Integr. Plant Biol. 49, 246-254.
    • (2007) J. Integr. Plant Biol. , vol.49 , pp. 246-254
    • Zhang, W.J.1    Zhou, J.2    Li, Z.F.3    Wang, L.4    Gu, X.5    Zhong, Y.6
  • 34
    • 70350344794 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage patterns in different plant mitochondrial genomes
    • Zhou M, Li X (2008) Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol. Biol. Rep. 36, 2039-2046.
    • (2008) Mol. Biol. Rep. , vol.36 , pp. 2039-2046
    • Zhou, M.1    Li, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.