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Volumn 7, Issue 10, 2012, Pages

Mutational Bias and Translational Selection Shaping the Codon Usage Pattern of Tissue-Specific Genes in Rice

Author keywords

[No Author keywords available]

Indexed keywords

ANTHER; ARTICLE; BRACHYPODIUM; CODON USAGE; CONTROLLED STUDY; CORRESPONDENCE ANALYSIS; EMBRYONAL TISSUE; ENDOSPERM; EVOLUTION; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC VARIABILITY; INTERNAL CORRESPONDENCE ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENOME; PLANT LEAF; PLANT ROOT; SEED PLANT; SHOOT; SORGHUM;

EID: 84868095970     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048295     Document Type: Article
Times cited : (30)

References (33)
  • 1
    • 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
  • 2
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
    • Duret L, Mouchiroud D, (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci U S A 96: 4482-4487.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 4482-4487
    • Duret, L.1    Mouchiroud, D.2
  • 3
  • 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: 640-669.
    • (2002) Curr Opin Genet Dev , vol.12 , pp. 640-669
    • Duret, L.1
  • 5
    • 4344647504 scopus 로고    scopus 로고
    • Tissue-specific codon usage and the expression of human genes
    • Plotkin JB, Robins H, Levine AJ, (2004) Tissue-specific codon usage and the expression of human genes. Proc Natl Acad Sci U S A 101: 12588-12591.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 12588-12591
    • Plotkin, J.B.1    Robins, H.2    Levine, A.J.3
  • 6
    • 33244484877 scopus 로고    scopus 로고
    • No evidence for tissue-specific adaptation of synonymous codon usage in humans
    • Sémon M, Lobry JR, Duret L, (2006) No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol Biol Evol 23: 523-529.
    • (2006) Mol Biol Evol , vol.23 , pp. 523-529
    • Sémon, M.1    Lobry, J.R.2    Duret, L.3
  • 7
    • 1542286776 scopus 로고    scopus 로고
    • Mammalian housekeeping genes evolve more slowly than tissue-specific genes
    • Zhang L, Li WH, (2004) Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol 21: 236-239.
    • (2004) Mol Biol Evol , vol.21 , pp. 236-239
    • Zhang, L.1    Li, W.H.2
  • 8
    • 59149093133 scopus 로고    scopus 로고
    • Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and Arabidopsis
    • Mukhopadhyay P, Basak S, Ghosh TC, (2008) Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and Arabidopsis. DNA Res 15: 347-356.
    • (2008) DNA Res , vol.15 , pp. 347-356
    • Mukhopadhyay, P.1    Basak, S.2    Ghosh, T.C.3
  • 10
    • 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
  • 11
    • 0043196689 scopus 로고
    • L'analyse des correspondances internes d'un tableau partitionné: Son usage en hydrobiology
    • Cazes P, Chessel D, Doledec S, (1988) L'analyse des correspondances internes d'un tableau partitionné: son usage en hydrobiology. Rev Stat Appl 36: 39-54.
    • (1988) Rev Stat Appl , vol.36 , pp. 39-54
    • Cazes, P.1    Chessel, D.2    Doledec, S.3
  • 13
    • 34547884302 scopus 로고    scopus 로고
    • Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice
    • Li M, Xu W, Yang W, Kong Z, Xue Y, (2007) Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice. Plant Physiol 144: 1797-1812.
    • (2007) Plant Physiol , vol.144 , pp. 1797-1812
    • Li, M.1    Xu, W.2    Yang, W.3    Kong, Z.4    Xue, Y.5
  • 14
    • 63349083143 scopus 로고    scopus 로고
    • Characterization and expression profiles of miRNAs in rice seeds
    • Xue LJ, Zhang JJ, Xue HW, (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 37: 916-930.
    • (2009) Nucleic Acids Res , vol.37 , pp. 916-930
    • Xue, L.J.1    Zhang, J.J.2    Xue, H.W.3
  • 16
    • 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
  • 17
    • 0023650543 scopus 로고
    • The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH, (1987) The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15: 1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 18
    • 0037109119 scopus 로고    scopus 로고
    • Use and misuse of correspondence analysis in codon usage studies
    • Perrière G, Thioulouse J, (2002) Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res 30: 4548-4555.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4548-4555
    • Perrière, G.1    Thioulouse, J.2
  • 19
    • 41149089793 scopus 로고    scopus 로고
    • SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis
    • In: Bastolla U, Porto M, Roman HE, Vendruscolo M, editors, Biological and Medical Physics, Biomedical Engineering
    • Charif D, Lobry JR (2007) SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Bastolla U, Porto M, Roman HE, Vendruscolo M, editors. Structural approaches to sequence evolution: Molecules, networks, populations. Biological and Medical Physics, Biomedical Engineering. p. 207-232.
    • (2007) Structural approaches to sequence evolution: Molecules, networks, populations , pp. 207-232
    • Charif, D.1    Lobry, J.R.2
  • 20
    • 37649024043 scopus 로고    scopus 로고
    • The ade4 package: implementing the duality diagram for ecologists
    • Dray S, Dufour AB, (2007) The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 22: 1-20.
    • (2007) J Stat Softw , vol.22 , pp. 1-20
    • Dray, S.1    Dufour, A.B.2
  • 22
    • 0038480747 scopus 로고    scopus 로고
    • Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria
    • Lobry J, Chessel D, (2003) Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J Appl Genet 44: 235-261.
    • (2003) J Appl Genet , vol.44 , pp. 235-261
    • Lobry, J.1    Chessel, D.2
  • 23
    • 0009183442 scopus 로고    scopus 로고
    • PhD Thesis, University of Nottingham, UK
    • Peden JF (1999) Analysis of codon usage. PhD Thesis, University of Nottingham, UK. p. 50-90.
    • (1999) Analysis of codon usage , pp. 50-90
    • Peden, J.F.1
  • 24
    • 78651300216 scopus 로고    scopus 로고
    • PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
    • Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, et al. (2011) PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res 39: D556-D560.
    • (2011) Nucleic Acids Res , vol.39
    • Huerta-Cepas, J.1    Capella-Gutierrez, S.2    Pryszcz, L.P.3    Denisov, I.4    Kormes, D.5
  • 25
    • 78651277241 scopus 로고    scopus 로고
    • MetaPhOrs: orthology and paralogy predictions from multiple phylogenetics evidence using a consistency-based confidence score
    • Pryszcz LP, Huerta-Cepas J, (2011) Gabaldón (2011) MetaPhOrs: orthology and paralogy predictions from multiple phylogenetics evidence using a consistency-based confidence score. Nucleic Acids Res 39: e32.
    • (2011) Nucleic Acids Res , vol.39
    • Pryszcz, L.P.1    Huerta-Cepas, J.2    Gabaldón3
  • 27
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski LB, Golding GB, (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52: 540-542.
    • (2001) J Mol Evol , vol.52 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 28
    • 77955019084 scopus 로고    scopus 로고
    • Parallelization of the MAFFT multiple sequence alignment program
    • Katoh K, Toh H, (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26: 1899-1900.
    • (2010) Bioinformatics , vol.26 , pp. 1899-1900
    • Katoh, K.1    Toh, H.2
  • 29
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z, Nielsen R, (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
    • (2000) Mol Biol Evol , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 30
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: phylogenetic analysis by maximum likelihood
    • Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 31
    • 84857872964 scopus 로고    scopus 로고
    • The use of EST expression matrixes for the quality control of gene expression data
    • Milnthorpe AT, Soloviev M, (2012) The use of EST expression matrixes for the quality control of gene expression data. PLoS One 7: e32966.
    • (2012) PLoS One , vol.7
    • Milnthorpe, A.T.1    Soloviev, M.2
  • 32
    • 0345411919 scopus 로고    scopus 로고
    • Isochores and tissue-specificity
    • Vinogradov AE, (2003) Isochores and tissue-specificity. Nucleic Acids Res 31: 5212-5220.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5212-5220
    • Vinogradov, A.E.1
  • 33
    • 0036613754 scopus 로고    scopus 로고
    • Clustering of housekeeping genes provides a unified model of gene order in the human genome
    • Lercher MJ, Urrutia AO, Hurst LD, (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31: 180-183.
    • (2002) Nat Genet , vol.31 , pp. 180-183
    • Lercher, M.J.1    Urrutia, A.O.2    Hurst, L.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.