메뉴 건너뛰기




Volumn 24, Issue 3, 2007, Pages 836-844

Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula

Author keywords

Codon bias; Gene expression; Populus; Translational selection

Indexed keywords

PROTEIN;

EID: 33847686233     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl212     Document Type: Article
Times cited : (122)

References (53)
  • 1
    • 0031593202 scopus 로고    scopus 로고
    • Codon bias evolution in Drosophila. Population genetics of mutation-selection drift
    • Akashi H. 1997. Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene. 205:269-278.
    • (1997) Gene , vol.205 , pp. 269-278
    • Akashi, H.1
  • 2
    • 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
  • 3
    • 0031738130 scopus 로고    scopus 로고
    • Translational selection and molecular evolution
    • Akashi H, Eyre-Walker A. 1998. Translational selection and molecular evolution. Curr Opin Genet Dev. 8:688-693.
    • (1998) Curr Opin Genet Dev , vol.8 , pp. 688-693
    • Akashi, H.1    Eyre-Walker, A.2
  • 4
    • 27144491328 scopus 로고    scopus 로고
    • Adaptive evolution of non-coding DNA in Drosophila
    • Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature. 437:1149-1152.
    • (2005) Nature , vol.437 , pp. 1149-1152
    • Andolfatto, P.1
  • 5
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova M, Bielawski JP, Yang ZH. 2001. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol. 18:1585-1592.
    • (2001) Mol Biol Evol , vol.18 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.H.3
  • 6
    • 0346991738 scopus 로고    scopus 로고
    • The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: Implications for the correlation between the synonymous substitution rate and codon usage bias
    • Bierne N, Eyre-Walker A. 2003. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics. 165:1587-1597.
    • (2003) Genetics , vol.165 , pp. 1587-1597
    • Bierne, N.1    Eyre-Walker, A.2
  • 7
    • 0344653653 scopus 로고    scopus 로고
    • Codon usage and gene function are related in sequences of Arabidopsis thaliana
    • Chiapello H, Fisacek F, Caboche M, Henaut A. 1998. Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene. 209:GC1-GC38.
    • (1998) Gene , vol.209
    • Chiapello, H.1    Fisacek, F.2    Caboche, M.3    Henaut, A.4
  • 8
    • 0034666040 scopus 로고    scopus 로고
    • Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
    • Coghlan A, Wolfe KH. 2000. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast. 16:1131-1145.
    • (2000) Yeast , vol.16 , pp. 1131-1145
    • Coghlan, A.1    Wolfe, K.H.2
  • 9
    • 0036263105 scopus 로고    scopus 로고
    • Population, evolutionary and genomic consequences of interference selection
    • Comeron JM, Kreitman M. 2002. Population, evolutionary and genomic consequences of interference selection. Genetics. 161:389-410.
    • (2002) Genetics , vol.161 , pp. 389-410
    • Comeron, J.M.1    Kreitman, M.2
  • 10
    • 0032894285 scopus 로고    scopus 로고
    • Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila
    • Comeron JM, Kreitman M, Aguade M. 1999. Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics. 151:239-249.
    • (1999) Genetics , vol.151 , pp. 239-249
    • Comeron, J.M.1    Kreitman, M.2    Aguade, M.3
  • 11
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond D, Raval A, Wilke C. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
    • (2006) Mol Biol Evol , vol.23 , pp. 327-337
    • Drummond, D.1    Raval, A.2    Wilke, C.3
  • 12
    • 0035155844 scopus 로고    scopus 로고
    • Substitution rates in Drosophila nuclear genes: Implications for translational selection
    • Dunn KA, Bielawski JP, Yang ZH. 2001. Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics. 157:295-305.
    • (2001) Genetics , vol.157 , pp. 295-305
    • Dunn, K.A.1    Bielawski, J.P.2    Yang, Z.H.3
  • 13
    • 0034237669 scopus 로고    scopus 로고
    • tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
    • Duret L. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 16:287-289.
    • (2000) Trends Genet , vol.16 , pp. 287-289
    • Duret, L.1
  • 14
    • 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
  • 15
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, Arabidopsis
    • Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, Arabidopsis. Proc Natl Acad Sci USA. 96:4482-4487.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 4482-4487
    • Duret, L.1    Mouchiroud, D.2
  • 16
    • 0033977618 scopus 로고    scopus 로고
    • Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
    • Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:68-74.
    • (2000) Mol Biol Evol , vol.17 , pp. 68-74
    • Duret, L.1    Mouchiroud, D.2
  • 18
    • 0033168465 scopus 로고    scopus 로고
    • Isochores result from mutation not selection
    • Francino HP, Ochman H. 1999. Isochores result from mutation not selection. Nature. 400:30-31.
    • (1999) Nature , vol.400 , pp. 30-31
    • Francino, H.P.1    Ochman, H.2
  • 19
    • 0028168856 scopus 로고
    • Codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N, Yang ZH. 1994. Codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol. 11:725-736.
    • (1994) Mol Biol Evol , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.H.2
  • 20
    • 1242296827 scopus 로고    scopus 로고
    • Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila
    • Halligan DL, Eyre-Walker A, Andolfatto P, Keightley PD. 2004. Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res. 14:273-279.
    • (2004) Genome Res , vol.14 , pp. 273-279
    • Halligan, D.L.1    Eyre-Walker, A.2    Andolfatto, P.3    Keightley, P.D.4
  • 21
    • 33745612972 scopus 로고    scopus 로고
    • Ubiquitous selective constrains in the Drosophila genome revealed by a genome-wide interspecies comparison
    • Halligan D, Keightley P. 2006. Ubiquitous selective constrains in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res. 16:875-884.
    • (2006) Genome Res , vol.16 , pp. 875-884
    • Halligan, D.1    Keightley, P.2
  • 22
    • 0022376704 scopus 로고
    • Dating the human-ape split by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, Yano T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
    • (1985) J Mol Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 23
    • 0030305457 scopus 로고    scopus 로고
    • R: A language for data analysis and graphics
    • Ihaka R, Gentleman R. 1996. R: a language for data analysis and graphics. J Comp Graph Stat. 5:299-314.
    • (1996) J Comp Graph Stat , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 24
    • 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
  • 25
    • 15544362769 scopus 로고    scopus 로고
    • Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae)
    • Ingvarsson PK. 2005. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics. 169:945-953.
    • (2005) Genetics , vol.169 , pp. 945-953
    • Ingvarsson, P.K.1
  • 26
    • 0034653294 scopus 로고    scopus 로고
    • Analysis of the yeast transcriptome with structural and functional categories: Characterizing highly expressed genes
    • Jansen R, Gerstein M. 2000. Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed genes. Nucleic Acids Res. 28:1481-1488.
    • (2000) Nucleic Acids Res , vol.28 , pp. 1481-1488
    • Jansen, R.1    Gerstein, M.2
  • 27
    • 0032882170 scopus 로고    scopus 로고
    • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
    • Kanaya S, Yamada Y, Kudo Y, Ikemura T. 1999. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene. 238:143-155.
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 28
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - the BLAST-like alignment tool
    • Kent WJ. 2002. BLAT - the BLAST-like alignment tool. Genome Res. 12:656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 29
    • 0028832984 scopus 로고
    • Functional constraints against variations on molecules from the tissue-level: Slowly evolving brain-specific genes demonstrated by protein-kinase and immunoglobulin supergene families
    • Kuma K, Iwabe N, Miyata T. 1995. Functional constraints against variations on molecules from the tissue-level: slowly evolving brain-specific genes demonstrated by protein-kinase and immunoglobulin supergene families. Mol Biol Evol. 12:123-130.
    • (1995) Mol Biol Evol , vol.12 , pp. 123-130
    • Kuma, K.1    Iwabe, N.2    Miyata, T.3
  • 30
    • 17744376961 scopus 로고    scopus 로고
    • Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length and number of protein-protein interactions
    • Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length and number of protein-protein interactions. Mol Biol Evol. 22:1345-1354.
    • (2005) Mol Biol Evol , vol.22 , pp. 1345-1354
    • Lemos, B.1    Bettencourt, B.R.2    Meiklejohn, C.D.3    Hartl, D.L.4
  • 31
    • 33749261964 scopus 로고    scopus 로고
    • Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes
    • Lin Y, Byrnes J, Hwang J, Li W. 2006. Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc Natl Acad Sci USA. 103:14412-14416.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 14412-14416
    • Lin, Y.1    Byrnes, J.2    Hwang, J.3    Li, W.4
  • 33
    • 11944249127 scopus 로고    scopus 로고
    • Correlated evolution of synonymous and nonsynonymous sites in Drosophila
    • Marais G, Domazet-Loso T, Tautz D, Charlesworth B. 2004. Correlated evolution of synonymous and nonsynonymous sites in Drosophila. J Mol Evol. 59:771-779.
    • (2004) J Mol Evol , vol.59 , pp. 771-779
    • Marais, G.1    Domazet-Loso, T.2    Tautz, D.3    Charlesworth, B.4
  • 34
    • 0035826858 scopus 로고    scopus 로고
    • Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes
    • Marais G, Mouchiroud D, Duret L. 2001. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci USA. 98:5688-5692.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5688-5692
    • Marais, G.1    Mouchiroud, D.2    Duret, L.3
  • 36
    • 0034099647 scopus 로고    scopus 로고
    • The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation
    • McVean GAT, Charlesworth B. 2000. The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics. 155:929-944.
    • (2000) Genetics , vol.155 , pp. 929-944
    • McVean, G.A.T.1    Charlesworth, B.2
  • 37
    • 0035157374 scopus 로고    scopus 로고
    • Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila
    • McVean GA, Vieira J. 2001. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics. 157:245-257.
    • (2001) Genetics , vol.157 , pp. 245-257
    • McVean, G.A.1    Vieira, J.2
  • 38
    • 0030731696 scopus 로고    scopus 로고
    • Codon usage bias and tRNA abundance in Drosophila
    • Moriyama EN, Powell JR. 1997. Codon usage bias and tRNA abundance in Drosophila. J Mol Evol. 45:514-523.
    • (1997) J Mol Evol , vol.45 , pp. 514-523
    • Moriyama, E.N.1    Powell, J.R.2
  • 39
    • 24744455048 scopus 로고
    • (11 co-authors). 2005. Substitution rate and structural divergence of 5′ UTR evolution: Comparative analysis between human and cynomolus monkey cDNAs
    • Osada N, Hirata M, Tanuma R, et al. (11 co-authors). 2005. Substitution rate and structural divergence of 5′ UTR evolution: comparative analysis between human and cynomolus monkey cDNAs. Mol Biol Evol. 22:1976-1982.
    • (1976) Mol Biol Evol , vol.22
    • Osada, N.1    Hirata, M.2    Tanuma, R.3
  • 40
    • 0035282838 scopus 로고    scopus 로고
    • Restricted wobble rules for eukaryotic genomes
    • Percudani R. 2001. Restricted wobble rules for eukaryotic genomes. Trends Genet. 17:133-135.
    • (2001) Trends Genet , vol.17 , pp. 133-135
    • Percudani, R.1
  • 41
    • 0030861159 scopus 로고    scopus 로고
    • Evolution of codon usage bias in Drosophila
    • Powell JR, Moriyama EN. 1997. Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA. 94:7784-7790.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 7784-7790
    • Powell, J.R.1    Moriyama, E.N.2
  • 43
    • 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
  • 44
    • 11144317388 scopus 로고    scopus 로고
    • Adaptive basis of codon usage in the haploid moss Physcomitrella patens
    • Stenoien HK. 2005. Adaptive basis of codon usage in the haploid moss Physcomitrella patens. Heredity. 94:87-93.
    • (2005) Heredity , vol.94 , pp. 87-93
    • Stenoien, H.K.1
  • 45
    • 4644282569 scopus 로고    scopus 로고
    • Sterky F, Bhalerao R, Unneberg P, et al. (19 co-authors). 2004. A Populus EST resource for plant functional genomics. Proc Natl Acad Sci USA. 101:13951-13956.
    • Sterky F, Bhalerao R, Unneberg P, et al. (19 co-authors). 2004. A Populus EST resource for plant functional genomics. Proc Natl Acad Sci USA. 101:13951-13956.
  • 46
    • 33748760611 scopus 로고    scopus 로고
    • Tuskan G, DiFazio S, Jansson S, et al. (111 co-authors). 2006. The genome of Black cottonwood Populus trichocarpa (Torr. & Gray). Science. 313:1596-1604.
    • Tuskan G, DiFazio S, Jansson S, et al. (111 co-authors). 2006. The genome of Black cottonwood Populus trichocarpa (Torr. & Gray). Science. 313:1596-1604.
  • 47
    • 33746913459 scopus 로고    scopus 로고
    • Analysis of 70000 EST sequences to study divergence between two closely related Populus species
    • Unneberg P, Strömberg M, Lundeberg J, Jansson S, Sterky F. 2005. Analysis of 70000 EST sequences to study divergence between two closely related Populus species. Tree Genet Genome. 1:109-115.
    • (2005) Tree Genet Genome , vol.1 , pp. 109-115
    • Unneberg, P.1    Strömberg, M.2    Lundeberg, J.3    Jansson, S.4    Sterky, F.5
  • 48
    • 0035671698 scopus 로고    scopus 로고
    • Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
    • Urrutia AO, Hurst LD. 2001. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics. 159:1191-1199.
    • (2001) Genetics , vol.159 , pp. 1191-1199
    • Urrutia, A.O.1    Hurst, L.D.2
  • 49
    • 0142092546 scopus 로고    scopus 로고
    • The signature of selection mediated by expression on human genes
    • Urrutia AO, Hurst LD. 2003. The signature of selection mediated by expression on human genes. Genome Res. 13:2260-2264.
    • (2003) Genome Res , vol.13 , pp. 2260-2264
    • Urrutia, A.O.1    Hurst, L.D.2
  • 51
    • 4143122090 scopus 로고    scopus 로고
    • Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
    • Wright SI, Yau CBK, 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    Yau, C.B.K.2    Looseley, M.3    Meyers, B.C.4
  • 52
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS. 13:555-556.
    • (1997) CABIOS , vol.13 , pp. 555-556
    • Yang, Z.1
  • 53
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang ZH, Nielsen R, Goldman N, Pedersen AMK. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.H.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.