메뉴 건너뛰기




Volumn 40, Issue 9, 2012, Pages 3834-3848

A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: Application to Saccharomyces cerevisiae natural strains

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CBK1 GENE; CCA1 GENE; CHS6 GENE; CYT1 GENE; DNA POLYMORPHISM; DUS1 GENE; EFT1 GENE; ESBP6 GENE; EXO5 GENE; FUNGAL GENE; FUNGAL GENOME; FUNGAL STRAIN; FZF1 GENE; GENE CLUSTER; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC SELECTION; GENETIC VARIABILITY; HAP4 GENE; IKS1 GENE; IMD4 GENE; IRC8 GENE; MATHEMATICAL COMPUTING; MLS1 GENE; MOLECULAR PHYLOGENY; NONHUMAN; NUP100 GENE; PDR10 GENE; PHD1 GENE; POPULATION STRUCTURE; PRIORITY JOURNAL; RME1 GENE; SACCHAROMYCES CEREVISIAE; SAS3 GENE; SSY1 GENE; SWH1 GENE; URN1 GENE; ZDS2 GENE;

EID: 84861393831     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks005     Document Type: Article
Times cited : (19)

References (38)
  • 2
    • 79952202465 scopus 로고    scopus 로고
    • Evolution of transcriptional regulatory networks in yeast populations
    • Cavalieri, D. (2010) Evolution of transcriptional regulatory networks in yeast populations. Wiley Interdiscip. Rev. Syst. Biol. Med., 2, 324-335.
    • (2010) Wiley Interdiscip. Rev. Syst. Biol. Med. , vol.2 , pp. 324-335
    • Cavalieri, D.1
  • 3
    • 77952245290 scopus 로고    scopus 로고
    • Divergence of nucleosome positioning between two closely related yeast species: Genetic basis and functional consequences
    • Tirosh, I., Sigal, N. and Barkai, N. (2010) Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol. Syst. Biol., 6, 365.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 365
    • Tirosh, I.1    Sigal, N.2    Barkai, N.3
  • 4
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • DOI 10.1038/nature01644
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254. (Pubitemid 40852689)
    • (2003) Nature , vol.423 , Issue.6937 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 5
    • 33745890277 scopus 로고    scopus 로고
    • Population structure and gene evolution in Saccharomyces cerevisiae
    • DOI 10.1111/j.1567-1364.2006.00059.x
    • Aa, E., Townsend, J.P., Adams, R.I., Nielsen, K.M. and Taylor, J.W. (2006) Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Res., 6, 702-715. (Pubitemid 44049990)
    • (2006) FEMS Yeast Research , vol.6 , Issue.5 , pp. 702-715
    • Aa, E.1    Townsend, J.P.2    Adams, R.I.3    Nielsen, K.M.4    Taylor, J.W.5
  • 6
    • 65449179200 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae: Population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates
    • Diezmann, S. and Dietrich, F.S. (2009) Saccharomyces cerevisiae: population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates. PLoS ONE, 4, 5317.
    • (2009) PLoS ONE , vol.4 , pp. 5317
    • Diezmann, S.1    Dietrich, F.S.2
  • 7
    • 33645096818 scopus 로고    scopus 로고
    • Evidence for domesticated and wild populations of Saccharomyces cerevisiae
    • Fay, J.C. and Benavides, J.A. (2005) Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet., 1, e5.
    • (2005) PLoS Genet. , vol.1
    • Fay, J.C.1    Benavides, J.A.2
  • 8
    • 0034760879 scopus 로고    scopus 로고
    • Molecular population genetics and evolution of a prion-like protein in saccharomyces cerevisiae
    • Jensen, M.A., True, H.L., Chernoff, Y.O. and Lindquist, S. (2001) Molecular population genetics and evolution of a prion-like protein in Saccharomyces cerevisiae. Genetics, 159, 527-535. (Pubitemid 33035097)
    • (2001) Genetics , vol.159 , Issue.2 , pp. 527-535
    • Jensen, M.A.1    True, H.L.2    Chernoff, Y.O.3    Lindquist, S.4
  • 9
    • 62649126517 scopus 로고    scopus 로고
    • Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae
    • Schacherer, J., Shapiro, J.A., Ruderfer, D.M. and Kruglyak, L. (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature, 458, 342-U103.
    • (2009) Nature , vol.458
    • Schacherer, J.1    Shapiro, J.A.2    Ruderfer, D.M.3    Kruglyak, L.4
  • 11
    • 34248192358 scopus 로고    scopus 로고
    • Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history
    • DOI 10.1111/j.1365-294X.2007.03266.x
    • Legras, J.-L., Merdinglu, D., Cornuet, J.-M. and Karst, F. (2007) Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol., 16, 2091-2102. (Pubitemid 46718913)
    • (2007) Molecular Ecology , vol.16 , Issue.10 , pp. 2091-2102
    • Legras, J.-L.1    Merdinoglu, D.2    Cornuet, J.-M.3    Karst, F.4
  • 13
    • 79952129813 scopus 로고    scopus 로고
    • Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae
    • Magwene, P.M., Kaykç, Ö., Granek, J.A., Reininga, J.M., Scholl, Z. and Murray, D. (2011) Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 108, 1987-1992.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 1987-1992
    • Magwene, P.M.1    Kaykç, Ö.2    Granek, J.A.3    Reininga, J.M.4    Scholl, Z.5    Murray, D.6
  • 14
    • 79952262678 scopus 로고    scopus 로고
    • Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae
    • Borneman, A.R., Desany, B.A., Riches, D., Affourtit, J.P., Forgan, A.H., Pretorius, I.S., Egholm, M. and Chambers, P.J. (2011) Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet., 7, e1001287.
    • (2011) PLoS Genet. , vol.7
    • Borneman, A.R.1    Desany, B.A.2    Riches, D.3    Affourtit, J.P.4    Forgan, A.H.5    Pretorius, I.S.6    Egholm, M.7    Chambers, P.J.8
  • 16
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 17
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (version 32)
    • Felsenstein, J. (1989) PHYLIP-Phylogeny Inference Package (version 32). Cladistics, 5, 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 19
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 23
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol., 15, 568-573. (Pubitemid 28194621)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.5 , pp. 568-573
    • Yang, Z.1
  • 24
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang, Z. and Nielsen, R. (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol., 17, 32-43. (Pubitemid 30056990)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.1 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 25
    • 48449101412 scopus 로고    scopus 로고
    • Standard and generalized McDonald-Kreitman test: A website to detect selection by comparing different classes of DNA sites
    • Egea, R., Casillas, S. and Barbadilla, A. (2008) Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. Nucleic Acids Res., 36, W157-W162.
    • (2008) Nucleic Acids Res. , vol.36
    • Egea, R.1    Casillas, S.2    Barbadilla, A.3
  • 26
    • 0023650543 scopus 로고
    • The codon adaptation index- A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P.M. and Li, W.-H. (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
  • 27
    • 0009183442 scopus 로고    scopus 로고
    • PhD Thesis Department of Genetics. University of Nottingham UK
    • Peden, J.F. (1999) Analysis of codon usage. PhD Thesis, Department of Genetics. University of Nottingham, UK.
    • (1999) Analysis of Codon Usage
    • Peden, J.F.1
  • 28
    • 0025988205 scopus 로고
    • Synonymous codon usage in Saccharomyces cerevisiae
    • Sharp, P.M. and Cowe, E. (1991) Synonymous codon usage in Saccharomyces cerevisiae. Yeast, 7, 657-678.
    • (1991) Yeast , vol.7 , pp. 657-678
    • Sharp, P.M.1    Cowe, E.2
  • 29
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald, J.H. and Kreitman, M. (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652-654. (Pubitemid 21896661)
    • (1991) Nature , vol.351 , Issue.6328 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 31
    • 79952276786 scopus 로고    scopus 로고
    • Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
    • Venkataram, S. and Fay, J.C. (2010) Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence? Genome Biol. Evol., 2, 851-858.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 851-858
    • Venkataram, S.1    Fay, J.C.2
  • 33
  • 34
    • 0031033277 scopus 로고    scopus 로고
    • Episodic adaptive evolution of primate lysozymes
    • DOI 10.1038/385151a0
    • Messier, W. and Stewart, C.-B. (1997) Episodic adaptive evolution of primate lysozymes. Nature, 385, 151-154. (Pubitemid 27034214)
    • (1997) Nature , vol.385 , Issue.6612 , pp. 151-154
    • Messier, W.1    Stewart, C.-B.2
  • 35
    • 0030992836 scopus 로고    scopus 로고
    • Rhodopsin evolution in the dark
    • Crandall, K.A. and Hillis, D.M. (1997) Rhodopsin evolution in the dark. Nature, 387, 667-668.
    • (1997) Nature , vol.387 , pp. 667-668
    • Crandall, K.A.1    Hillis, D.M.2
  • 36
    • 44849142385 scopus 로고    scopus 로고
    • Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae
    • DOI 10.1111/j.1365-294X.2008.03765.x
    • Brown, K.M., Landry, C.R., Hartl, D.L. and Cavalieri, D. (2008) Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol. Ecol., 17, 2985-2997. (Pubitemid 351793525)
    • (2008) Molecular Ecology , vol.17 , Issue.12 , pp. 2985-2997
    • Brown, K.M.1    Landry, C.R.2    Hartl, D.L.3    Cavalieri, D.4
  • 37
    • 0037238176 scopus 로고    scopus 로고
    • Domestication of wild Saccharomyces cerevisiae is accompanied by changes in gene expression and colony morphology
    • DOI 10.1046/j.1365-2958.2003.03332.x
    • Kuthan, M., Devaux, F., Janderová, B., Slaninová, I., Jacq, C. and Palková, Z. (2003) Domestication of wild Saccharomyces cerevisiae is accompanied by changes in gene expression and colony morphology. Mol. Microbiol., 47, 745-754. (Pubitemid 36114982)
    • (2003) Molecular Microbiology , vol.47 , Issue.3 , pp. 745-754
    • Kuthan, M.1    Devaux, F.2    Janderova, B.3    Slaninova, I.4    Jacq, C.5    Palkova, Z.6
  • 38
    • 41549089929 scopus 로고    scopus 로고
    • Yeast and fungal morphogenesis from an evolutionary perspective
    • Wedlich-Soldner, R. and Li, R. (2008) Yeast and fungal morphogenesis from an evolutionary perspective. Semin. Cell Dev. Biol., 19, 224-233.
    • (2008) Semin. Cell Dev. Biol. , vol.19 , pp. 224-233
    • Wedlich-Soldner, R.1    Li, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.