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Volumn 27, Issue 4, 2010, Pages 800-810

Modal codon usage: Assessing the typical codon usage of a genome

Author keywords

Codon adaptation index; Correspondence analysis; Horizontal gene transfer

Indexed keywords

ARCHAEAL GENOME; BACTERIAL GENOME; BORRELIA BURGDORFERI; CHROMOSOME; CODON USAGE; CONTROLLED STUDY; DNA REPLICATION; DNA STRAND; GENETIC TRANSCRIPTION; MOLECULAR EVOLUTION; NONHUMAN; PLASMID; REVIEW; RHIZOBIUM RADIOBACTER; ARTICLE; BACTERIAL CHROMOSOME; CODON; GENETICS; PHYLOGENY; REPLICON;

EID: 77952314202     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp281     Document Type: Review
Times cited : (37)

References (42)
  • 1
    • 0036842986 scopus 로고    scopus 로고
    • Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia
    • DOI 10.1038/ng986
    • Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S. 2002. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet. 32:402-407. (Pubitemid 35266115)
    • (2002) Nature Genetics , vol.32 , Issue.3 , pp. 402-407
    • Akman, L.1    Yamashita, A.2    Watanabe, H.3    Oshima, K.4    Shiba, T.5    Hattori, M.6    Aksoy, S.7
  • 2
    • 0030829566 scopus 로고    scopus 로고
    • Thermosipho melanesiensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the Southwestern Pacific Ocean
    • Antoine E, Cilia V, Muenier JR, Guezennec J, Lesongeur F, Barbier G. 1997. Thermosipho melanesiensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the Southwestern Pacific Ocean. Int J Syst Bacteriol. 47:1118-1123. (Pubitemid 27441241)
    • (1997) International Journal of Systematic Bacteriology , vol.47 , Issue.4 , pp. 1118-1123
    • Antoine, E.1    Cilia, V.2    Meunier, J.R.3    Guezennec, J.4    Lesongeur, F.5    Barbier, G.6
  • 4
    • 0027292427 scopus 로고
    • Linear DNA of Borrelia species and antigenic variation
    • DOI 10.1016/0966-842X(93)90139-I
    • Barbour AG. 1993. Linear DNA of Borrelia species and antigenic variation. Trends Microbiol. 1:236-239. (Pubitemid 23257651)
    • (1993) Trends in Microbiology , vol.1 , Issue.6 , pp. 236-239
    • Barbour, A.G.1
  • 6
    • 0036717992 scopus 로고    scopus 로고
    • A new type iv secretion system promotes conjugal transfer in agrobacterium tumefaciens
    • Chen L, Chen Y, Wood DW, Nester EW. 2002. A new type IV secretion system promotes conjugal transfer in Agrobacterium tumefaciens. J Bacteriol. 17:4838-4845.
    • (2002) J Bacteriol. , vol.17 , pp. 4838-4845
    • Chen, L.1    Chen, Y.2    Wood, D.W.3    Nester, E.W.4
  • 7
    • 0000122573 scopus 로고
    • Phylip-phylogeny inference package (version 3.2
    • Felsenstein J. 1989. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 8
    • 0031470826 scopus 로고    scopus 로고
    • Genomic sequence of a lyme disease spirochaete
    • 38 co-Authors
    • Fraser CM, Casjens S, Huang WM, et al. (38 co-Authors). 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-590.
    • (1997) Borrelia burgdorferi. Nature , vol.390 , pp. 580-590
    • Fraser, C.M.1    Casjens, S.2    Huang, W.M.3
  • 9
    • 0017616405 scopus 로고
    • Ti plasmids of Agrobacterium as conjugative plasmids
    • DOI 10.1038/265561a0
    • Genetello C, Van Larebeke N, Holsters M, De Picker A, Van Montagu M, Schell J. 1977. Ti plasmids of Agrobacterium as conjugative plasmids. Nature 265:561-563. (Pubitemid 8035737)
    • (1977) Nature , vol.265 , Issue.5594 , pp. 561-563
    • Genetello, C.1    Van Larebeke, N.2    Holsters, M.3
  • 11
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy M, Gautier C. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 22:7055-7074.
    • (1982) Nucleic Acids Res. , vol.22 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 12
    • 0019188794 scopus 로고
    • Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type
    • Grantham R, Gautier C, Gouy M. 1980. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 8:1893-1912. (Pubitemid 10060230)
    • (1980) Nucleic Acids Research , vol.8 , Issue.9 , pp. 1893-1912
    • Grantham, R.1    Gautier, C.2    Gouy, M.3
  • 13
    • 0019519371 scopus 로고
    • Codon catalog usage is a genome strategy modulated for gene expressivity
    • Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R. 1981. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 9:r43-r74. (Pubitemid 11128643)
    • (1981) Nucleic Acids Research , vol.9 , Issue.1
    • Grantham, R.1    Gautier, C.2    Gouy, M.3
  • 14
    • 0018879196 scopus 로고
    • Codon catalog usage and the genome hypothesis
    • Grantham R, Gautier C, Gouy M, Mercier R, Pave A. 1980. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8:r49-r62. (Pubitemid 10154683)
    • (1980) Nucleic Acids Research , vol.8 , Issue.1
    • Grantham, R.1    Gautier, C.2    Gouy, M.3
  • 15
    • 0036572274 scopus 로고    scopus 로고
    • Synonymous codon usage in Pseudomonas aeruginosa PA01
    • DOI 10.1016/S0378-1119(02)00503-6, PII S0378111902005036
    • Grocock RJ, Sharp PM. 2002. Synonymous codon usage in Pseudomonas aeruginosa PA01. Gene. 289:131-139. (Pubitemid 34564493)
    • (2002) Gene , vol.289 , Issue.1-2 , pp. 131-139
    • Grocock, R.J.1    Sharp, P.M.2
  • 16
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes
    • DOI 10.1016/0378-1119(82)90157-3
    • Grosjean H, Fiers W. 1982. Preferential codon usage in prokaryotic genes: the optimal codon-Anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 18:199-209. (Pubitemid 13232993)
    • (1982) Gene , vol.18 , Issue.3 , pp. 199-209
    • Grosjean, H.1    Fiers, W.2
  • 17
    • 0141814791 scopus 로고    scopus 로고
    • Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia
    • Herbeck J, Wall D, Wernegreen J. 2003. Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology. 149: 2585-2596. (Pubitemid 37160732)
    • (2003) Microbiology , vol.149 , Issue.9 , pp. 2585-2596
    • Herbeck, J.T.1    Wall, D.P.2    Wernegreen, J.J.3
  • 18
    • 0019474499 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
    • DOI 10.1016/0022-2836(81)90363-6
    • Ikemura T. 1981a. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 146:1-21. (Pubitemid 11144185)
    • (1981) Journal of Molecular Biology , vol.146 , Issue.1 , pp. 1-21
    • Ikemura, T.1
  • 19
    • 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 optimal for the E. coli translational system
    • Ikemura T. 1981b. 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 optimal for the E. coli translational system. J Mol Biol. 151: 389-409. (Pubitemid 12252691)
    • (1981) Journal of Molecular Biology , vol.151 , Issue.3 , pp. 389-409
    • Ikemura, T.1
  • 20
    • 0033816775 scopus 로고    scopus 로고
    • Predicted highly expressed genes of diverse prokaryotic genomes
    • Karlin S, Mrázek J. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol. 182:5238-5250.
    • (2000) J Bacteriol. , vol.182 , pp. 5238-5250
    • Karlin, S.1    Mrázek, J.2
  • 22
    • 0017619818 scopus 로고
    • Transfer of virulence in vivo and in vitro in Agrobacterium
    • DOI 10.1038/265560a0
    • Kerr A, Manigault P, Tempe J. 1977. Transfer of virulence in vivo and in vitro in Agrobacterium. Nature 256:560-561. (Pubitemid 8035736)
    • (1977) Nature , vol.265 , Issue.5594 , pp. 560-561
    • Kerr, A.1    Manigault, P.2    Tempe, J.3
  • 23
    • 0033118273 scopus 로고    scopus 로고
    • Proteome composition and codon usage in spirochaetes: Species-specific and DNA strand-specific mutational biases
    • DOI 10.1093/nar/27.7.1642
    • Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. 1999. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 27:1642-1649. (Pubitemid 29209540)
    • (1999) Nucleic Acids Research , vol.27 , Issue.7 , pp. 1642-1649
    • Lafay, B.1    Lloyd, A.T.2    McLean, M.J.3    Devine, K.M.4    Sharp, P.M.5    Wolfe, K.H.6
  • 24
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • DOI 10.1007/PL00006158
    • Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 44:383-397. (Pubitemid 27161335)
    • (1997) Journal of Molecular Evolution , vol.44 , Issue.4 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 28
    • 0031851853 scopus 로고    scopus 로고
    • GCUA: General codon usage analysis
    • McInerney JO. 1998b. GCUA: general codon usage analysis. Bioinformatics 14:372-373. (Pubitemid 28393803)
    • (1998) Bioinformatics , vol.14 , Issue.4 , pp. 372-373
    • McInerney, J.O.1
  • 30
    • 0032870941 scopus 로고    scopus 로고
    • Codon usage and lateral gene transfer in Bacillus subtilis
    • DOI 10.1016/S1369-5274(99)00011-9
    • Moszer I, Rocha EPC, Danchin A. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr Opin Microbiol. 2:524-528. (Pubitemid 29477181)
    • (1999) Current Opinion in Microbiology , vol.2 , Issue.5 , pp. 524-528
    • Moszer, I.1    Rocha, E.P.2    Danchin, A.3
  • 31
    • 0000238336 scopus 로고
    • A simplex method for function minimization
    • Nelder J, Mead R. 1965. A simplex method for function minimization. Comput J. 7:308-313.
    • (1965) Comput J. , vol.7 , pp. 308-313
    • Nelder, J.1    Mead, R.2
  • 32
    • 0026488056 scopus 로고
    • Lowpassage- associated proteins of borrelia burgdorferi b31: Characterization and molecular cloning of ospd, a surface-exposed, plasmid-encoded lipoprotein
    • Norris SJ, Carter CJ, Howell JK, Barbour AG. 1992. Lowpassage- associated proteins of Borrelia burgdorferi B31: characterization and molecular cloning of OspD, a surface-exposed, plasmid-encoded lipoprotein. Infect Immun. 60:4662-4672.
    • (1992) Infect Immun. , vol.60 , pp. 4662-4672
    • Norris, S.J.1    Carter, C.J.2    Howell, J.K.3    Barbour, A.G.4
  • 35
    • 0032898516 scopus 로고    scopus 로고
    • Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome
    • DOI 10.1046/j.1365-2958.1999.01368.x
    • Picardeau M, Lobry JR, Hinnebusch BJ. 1999. Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome.Mol Microbiol. 32:437-445. (Pubitemid 29178708)
    • (1999) Molecular Microbiology , vol.32 , Issue.2 , pp. 437-445
    • Picardeau, M.1    Lobry, J.R.2    Hinnebusch, B.J.3
  • 36
    • 0347135951 scopus 로고    scopus 로고
    • Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids
    • DOI 10.1101/gr.1358104
    • Rispe C, Delmotte F, van Ham R, Moya A. 2004. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res. 14:44-53. (Pubitemid 38088524)
    • (2004) Genome Research , vol.14 , Issue.1 , pp. 44-53
    • Rispe, C.1    Delmotte, F.2    Van Ham, R.C.H.J.3    Moya, A.4
  • 37
    • 0036946946 scopus 로고    scopus 로고
    • Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado
    • DOI 10.1128/AEM.68.12.6013-6020.2002
    • Roh Y, Liu SV, Li G, Huang H, Phelps TJ, Zhou J. 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. Appl Environ Microbiol. 68:6013-6020. (Pubitemid 36342435)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.12 , pp. 6013-6020
    • Roh, Y.1    Liu, S.V.2    Li, G.3    Huang, H.4    Phelps, T.J.5    Zhou, J.6
  • 38
    • 0023650543 scopus 로고
    • The codon adaptation index-A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li W. 1987. The codon adaptation index-A measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 29:1281-1295.
    • (1987) Nucleic Acids Res. , vol.29 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.2
  • 39
    • 34250629241 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: Gene content and organization
    • DOI 10.1007/s11120-006-9122-4, Govindjee Special Issue: Part A, Celebrating Govindjee's 50 Years in Photosynthesis Research and his 75th Birthday
    • Sugita C, Ogata K, Shikata M, Jikuya H, Takano J, Furumichi M, Kanehisa M, Omata T, Sugiura M, Sugita M. 2007. Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. Photosyn Res. 93:55-67. (Pubitemid 47310276)
    • (2007) Photosynthesis Research , vol.93 , Issue.1-3 , pp. 55-67
    • Sugita, C.1    Ogata, K.2    Shikata, M.3    Jikuya, H.4    Takano, J.5    Furumichi, M.6    Kanehisa, M.7    Omata, T.8    Sugiura, M.9    Sugita, M.10
  • 42
    • 0001886802 scopus 로고
    • Probability functions
    • In: Abramowitz M, Stegun IA, editors. New York: Dover Publications
    • Zelen M, Severo N. 1965. Probability functions. In: Abramowitz M, Stegun IA, editors. Handbook of mathematical functions. New York: Dover Publications, p. 925-995.
    • (1965) Handbook of Mathematical Functions , pp. 925-995
    • Zelen, M.1    Severo, N.2


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