메뉴 건너뛰기




Volumn 31, Issue 12, 2014, Pages 3184-3193

Comparative genomics as a time machine: How relative gene dosage and metabolic requirements shaped the time-dependent resolution of yeast polyploidy

Author keywords

gene dosage; metabolic flux; polyploidy; protein interaction network; Saccharomyces cerevisiae; transcriptional regulatory network

Indexed keywords

FUNGAL DNA; FUNGAL PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84925003517     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu250     Document Type: Article
Times cited : (35)

References (64)
  • 1
    • 84859897319 scopus 로고    scopus 로고
    • Rarely successful polyploids and their legacy in plant genomes
    • Arrigo N, Barker MS. 2012. Rarely successful polyploids and their legacy in plant genomes. Curr Opin Plant Biol. 15:140-146.
    • (2012) Curr Opin Plant Biol. , vol.15 , pp. 140-146
    • Arrigo, N.1    Barker, M.S.2
  • 3
    • 79959858471 scopus 로고    scopus 로고
    • Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative followed by absolute dosage constraints
    • BekaertM, Edger PP, Pires JC, Conant GC. 2011. Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative followed by absolute dosage constraints. Plant Cell 23: 1719-1728.
    • (2011) Plant Cell , vol.23 , pp. 1719-1728
    • Bekaert, M.1    Edger, P.P.2    Pires, J.C.3    Conant, G.C.4
  • 4
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat. 57:289-300.
    • (1995) J R Stat Soc Series B Stat. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 5
    • 84866294456 scopus 로고    scopus 로고
    • Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines
    • Birchler JA, Veitia RA. 2012. Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A. 109:14746-14753.
    • (2012) Proc Natl Acad Sci U S A. , vol.109 , pp. 14746-14753
    • Birchler, J.A.1    Veitia, R.A.2
  • 6
    • 15044342010 scopus 로고    scopus 로고
    • Metabolic-flux and network analysis of fourteen hemiascomycetous yeasts
    • Blank LM, Lehmbeck F, Sauer U. 2005. Metabolic-flux and network analysis of fourteen hemiascomycetous yeasts. FEMS Yeast Res. 5: 545-558.
    • (2005) FEMS Yeast Res. , vol.5 , pp. 545-558
    • Blank, L.M.1    Lehmbeck, F.2    Sauer, U.3
  • 8
    • 25844471721 scopus 로고    scopus 로고
    • The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species
    • Byrne KP, Wolfe KH. 2005. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15:1456-1461.
    • (2005) Genome Res. , vol.15 , pp. 1456-1461
    • Byrne, K.P.1    Wolfe, K.H.2
  • 9
    • 36749056855 scopus 로고    scopus 로고
    • The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations
    • Charlesworth J, Eyre-Walker A. 2007. The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proc Natl Acad Sci U S A. 104:16992-16997.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 16992-16997
    • Charlesworth, J.1    Eyre-Walker, A.2
  • 12
    • 77950290826 scopus 로고    scopus 로고
    • Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast
    • Conant GC. 2010. Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast. Proc Biol Sci. 277: 869-876.
    • (2010) Proc Biol Sci. , vol.277 , pp. 869-876
    • Conant, G.C.1
  • 13
    • 84901818848 scopus 로고    scopus 로고
    • Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time
    • Conant GC, Birchler JA, Pires JC. 2014. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Curr Opin Plant Biol. 19:91-98.
    • (2014) Curr Opin Plant Biol. , vol.19 , pp. 91-98
    • Conant, G.C.1    Birchler, J.A.2    Pires, J.C.3
  • 14
    • 34547611439 scopus 로고    scopus 로고
    • Increased glycolytic flux as an outcome of whole-genome duplication in yeast
    • Conant GC, Wolfe KH. 2007. Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol Syst Biol. 3:129.
    • (2007) Mol Syst Biol. , vol.3 , pp. 129
    • Conant, G.C.1    Wolfe, K.H.2
  • 15
    • 52049091231 scopus 로고    scopus 로고
    • Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast
    • Conant GC, Wolfe KH. 2008. Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. Genetics 179:1681-1692.
    • (2008) Genetics , vol.179 , pp. 1681-1692
    • Conant, G.C.1    Wolfe, K.H.2
  • 17
    • 0002806690 scopus 로고    scopus 로고
    • OpenMP: An industry standard API for shared-memory programming
    • Dagum L, Menon R. 1998. OpenMP: an industry standard API for shared-memory programming. IEEE Comput Sci Eng. 5:46-55.
    • (1998) IEEE Comput Sci Eng. , vol.5 , pp. 46-55
    • Dagum, L.1    Menon, R.2
  • 20
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • Duarte NC, Herrgard MJ, Palsson BØ. 2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14:1298-1309.
    • (2004) Genome Res. , vol.14 , pp. 1298-1309
    • Duarte, N.C.1    Herrgard, M.J.2    Palsson B.Ø.3
  • 22
    • 70349682921 scopus 로고    scopus 로고
    • Gene and genome duplications: The impact of dosage sensitivity on the fate of nuclear genes
    • Edger PP, Pires JC. 2009. Gene and genome duplications: the impact of dosage sensitivity on the fate of nuclear genes. Chromosome Res. 17: 699-717.
    • (2009) Chromosome Res. , vol.17 , pp. 699-717
    • Edger, P.P.1    Pires, J.C.2
  • 23
    • 79952199263 scopus 로고    scopus 로고
    • Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling
    • Evangelisti AM, Conant GC. 2010. Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling. Genome Biol Evol. 2:826-834.
    • (2010) Genome Biol Evol. , vol.2 , pp. 826-834
    • Evangelisti, A.M.1    Conant, G.C.2
  • 24
    • 65249143921 scopus 로고    scopus 로고
    • Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event
    • Fawcett JA, Maere S, Van de Peer Y. 2009. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A. 106:5737-5742.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 5737-5742
    • Fawcett, J.A.1    Maere, S.2    Van De Peer, Y.3
  • 25
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
    • (1981) J Mol Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 26
    • 0030034795 scopus 로고    scopus 로고
    • A hidden markov model approach to variation among sites in rate of evolution
    • Felsenstein J, Churchill GA. 1996. A hidden markov model approach to variation among sites in rate of evolution. Mol Biol Evol. 13: 93-104.
    • (1996) Mol Biol Evol. , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 27
    • 67651039811 scopus 로고    scopus 로고
    • Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition
    • Freeling M. 2009. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu Rev Plant Biol. 60:433-453.
    • (2009) Annu Rev Plant Biol. , vol.60 , pp. 433-453
    • Freeling, M.1
  • 28
    • 33745610025 scopus 로고    scopus 로고
    • Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
    • Freeling M, Thomas BC. 2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16:805-814.
    • (2006) Genome Res. , vol.16 , pp. 805-814
    • Freeling, M.1    Thomas, B.C.2
  • 29
    • 77952980875 scopus 로고    scopus 로고
    • Ordered structure of the transcription network inherited from the yeast whole-genome duplication
    • Fusco D, Grassi L, Bassetti B, Caselle M, Cosentino Lagomarsino M. 2010. Ordered structure of the transcription network inherited from the yeast whole-genome duplication. BMC Syst Biol. 4:77.
    • (2010) BMC Syst Biol. , vol.4 , pp. 77
    • Fusco, D.1    Grassi, L.2    Bassetti, B.3    Caselle, M.4    Cosentino Lagomarsino, M.5
  • 32
    • 67149106149 scopus 로고    scopus 로고
    • Additions, losses and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome
    • Gordon JL, Byrne KP, Wolfe KH. 2009. Additions, losses and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet. 5: e1000485.
    • (2009) PLoS Genet. , vol.5 , pp. e1000485
    • Gordon, J.L.1    Byrne, K.P.2    Wolfe, K.H.3
  • 33
    • 66049128566 scopus 로고    scopus 로고
    • Distinguishing among evolutionary models for the maintenance of gene duplicates
    • Hahn MW. 2009. Distinguishing among evolutionary models for the maintenance of gene duplicates. J Hered. 100:605-617.
    • (2009) J Hered. , vol.100 , pp. 605-617
    • Hahn, M.W.1
  • 35
    • 35148863240 scopus 로고    scopus 로고
    • Gene duplication and the adaptive evolution of a classic genetic switch
    • Hittinger CT, Carroll SB. 2007. Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677-681.
    • (2007) Nature , vol.449 , pp. 677-681
    • Hittinger, C.T.1    Carroll, S.B.2
  • 37
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    • Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624.
    • (2004) Nature , vol.428 , pp. 617-624
    • Kellis, M.1    Birren, B.W.2    Lander, E.S.3
  • 38
    • 66649120205 scopus 로고    scopus 로고
    • Differential subcellular localization of ribosomal protein L7 paralogs in Saccharomyces cerevisiae
    • Kim T-Y, Ha CW, Huh W-K. 2009. Differential subcellular localization of ribosomal protein L7 paralogs in Saccharomyces cerevisiae. Mol Cells. 27:539-546.
    • (2009) Mol Cells. , vol.27 , pp. 539-546
    • Kim, T.-Y.1    Ha, C.W.2    Huh, W.-K.3
  • 39
    • 35548973466 scopus 로고    scopus 로고
    • Functional specificity among ribosomal proteins regulates gene expression
    • Komili S, Farny NG, Roth FP, Silver PA. 2007. Functional specificity among ribosomal proteins regulates gene expression. Cell 131: 557-571.
    • (2007) Cell , vol.131 , pp. 557-571
    • Komili, S.1    Farny, N.G.2    Roth, F.P.3    Silver, P.A.4
  • 40
    • 0035527396 scopus 로고    scopus 로고
    • A likelihood approach to estimating phylogeny from discrete morphological character data
    • Lewis PO. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol. 50:913-925.
    • (2001) Syst Biol. , vol.50 , pp. 913-925
    • Lewis, P.O.1
  • 44
    • 33846849322 scopus 로고    scopus 로고
    • Fermentative lifestyle in yeastsbelonging totheSaccharomyces complex
    • Merico A, Sulo P, Piskur J, Compagno C. 2007. Fermentative lifestyle in yeastsbelonging totheSaccharomyces complex.FEBS J. 274:976-989.
    • (2007) FEBS J. , vol.274 , pp. 976-989
    • Merico, A.1    Sulo, P.2    Piskur, J.3    Compagno, C.4
  • 46
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • Papp B, Pal C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.
    • (2003) Nature , vol.424 , pp. 194-197
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 47
    • 80054012758 scopus 로고    scopus 로고
    • Patterns of indirect protein interactions suggest a spatial organization to metabolism
    • Perez-Bercoff.A, McLysaght A, Conant GC. 2011. Patterns of indirect protein interactions suggest a spatial organization to metabolism. Mol Biosyst. 7:3056-3064.
    • (2011) Mol Biosyst. , vol.7 , pp. 3056-3064
    • Perez-Bercoff, A.1    McLysaght, A.2    Conant, G.C.3
  • 50
    • 79957788300 scopus 로고    scopus 로고
    • Measuring the evolutionary rate of protein-protein interaction
    • Qian W, He X, Chan E, Xu H, Zhang J. 2011. Measuring the evolutionary rate of protein-protein interaction. Proc Natl Acad Sci U S A. 108: 8725-8730.
    • (2011) Proc Natl Acad Sci U S A. , vol.108 , pp. 8725-8730
    • Qian, W.1    He, X.2    Chan, E.3    Xu, H.4    Zhang, J.5
  • 52
    • 33645023614 scopus 로고    scopus 로고
    • Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
    • Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH. 2006. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345.
    • (2006) Nature , vol.440 , pp. 341-345
    • Scannell, D.R.1    Byrne, K.P.2    Gordon, J.L.3    Wong, S.4    Wolfe, K.H.5
  • 53
    • 34347209089 scopus 로고    scopus 로고
    • Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
    • Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M, Wolfe KH. 2007. Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci U S A. 104:8397-8402.
    • (2007) Proc Natl Acad Sci U S A. , vol.104 , pp. 8397-8402
    • Scannell, D.R.1    Frank, A.C.2    Conant, G.C.3    Byrne, K.P.4    Woolfit, M.5    Wolfe, K.H.6
  • 54
    • 38049038829 scopus 로고    scopus 로고
    • A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast
    • Scannell DR,Wolfe KH. 2008. A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Genome Res. 18:137-147.
    • (2008) Genome Res. , vol.18 , pp. 137-147
    • Scannell, D.R.1    Wolfe, K.H.2
  • 55
    • 84859917501 scopus 로고    scopus 로고
    • Ancient whole genome duplications, novelty and diversification: The WGD Radiation Lag-Time Model
    • Schranz ME, Mohammadin S, Edger PP. 2012. Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model. Curr Opin Plant Biol. 15:147-153.
    • (2012) Curr Opin Plant Biol. , vol.15 , pp. 147-153
    • Schranz, M.E.1    Mohammadin, S.2    Edger, P.P.3
  • 56
    • 0032879798 scopus 로고    scopus 로고
    • Yeast genome evolution in the post-genome era
    • Seoighe C, Wolfe KH. 1999. Yeast genome evolution in the post-genome era. Curr Opin Microbiol. 2:548-554.
    • (1999) Curr Opin Microbiol. , vol.2 , pp. 548-554
    • Seoighe, C.1    Wolfe, K.H.2
  • 59
    • 70349325524 scopus 로고    scopus 로고
    • The evolutionary significance of ancient genome duplications
    • Van de Peer Y, Maere S, Meyer A. 2009. The evolutionary significance of ancient genome duplications. Nat Rev Genet. 10:725-732.
    • (2009) Nat Rev Genet. , vol.10 , pp. 725-732
    • Van De Peer, Y.1    Maere, S.2    Meyer, A.3
  • 60
    • 73349113515 scopus 로고    scopus 로고
    • Metabolic adaptation after whole genome duplication
    • van Hoek MJ, Hogeweg P. 2009. Metabolic adaptation after whole genome duplication. Mol Biol Evol. 26:2441-2453.
    • (2009) Mol Biol Evol. , vol.26 , pp. 2441-2453
    • Van Hoek, M.J.1    Hogeweg, P.2
  • 61
    • 73949089947 scopus 로고    scopus 로고
    • Dominance and gene dosage balance in health and disease: Why levels matter!
    • Veitia RA, Birchler JA. 2010. Dominance and gene dosage balance in health and disease: why levels matter!. J Pathol. 220:174-185.
    • (2010) J Pathol. , vol.220 , pp. 174-185
    • Veitia, R.A.1    Birchler, J.A.2
  • 63
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713.
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 64
    • 84889021742 scopus 로고    scopus 로고
    • Evolution after whole-genome duplication: A network perspective
    • Zhu Y, Lin Z, Nakhleh L. 2013. Evolution after whole-genome duplication: a network perspective. G3 3:2049-2057.
    • (2013) G3 , vol.3 , pp. 2049-2057
    • Zhu, Y.1    Lin, Z.2    Nakhleh, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.