메뉴 건너뛰기




Volumn 6, Issue , 2006, Pages

A systematic search for positive selection in higher plants (Embryophytes)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA; MAGNOLIOPHYTA;

EID: 33747239595     PISSN: 14712229     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-6-12     Document Type: Article
Times cited : (72)

References (64)
  • 1
    • 0034914764 scopus 로고    scopus 로고
    • Perspective: From mutants to mechanisms? Assessing the candidate gene paradigm in evolutionary biology
    • Haag ES, True JR: Perspective: From mutants to mechanisms? Assessing the candidate gene paradigm in evolutionary biology. Evolution 2001, 55:1077-1084.
    • (2001) Evolution , vol.55 , pp. 1077-1084
    • Haag, E.S.1    True, J.R.2
  • 4
    • 0034707210 scopus 로고    scopus 로고
    • Evolution of gene families
    • Ohta T: Evolution of gene families. Gene 2000, 259:45-52.
    • (2000) Gene , vol.259 , pp. 45-52
    • Ohta, T.1
  • 5
    • 10344222111 scopus 로고    scopus 로고
    • Molecular population genetics of redundant floral- regulatory genes in Arabidopsis thaliana
    • Moore RC, Grant SR, Purugganan MD: Molecular population genetics of redundant floral- regulatory genes in Arabidopsis thaliana. Molecular Biology and Evolution 2005, 22:91-103.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 91-103
    • Moore, R.C.1    Grant, S.R.2    Purugganan, M.D.3
  • 6
    • 20044369186 scopus 로고    scopus 로고
    • An adaptive radiation model for the origin of new gene functions
    • Francino MP: An adaptive radiation model for the origin of new gene functions. Nature Genetics 2005, 37:573-577.
    • (2005) Nature Genetics , vol.37 , pp. 573-577
    • Francino, M.P.1
  • 7
    • 21344439563 scopus 로고    scopus 로고
    • Subfunctionalization of duplicated genes as a transition state to neofunctionalization
    • Rastogi S, Liberles DA: Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evolutionary Biology 2005, 5:28.
    • (2005) BMC Evolutionary Biology , vol.5 , pp. 28
    • Rastogi, S.1    Liberles, D.A.2
  • 8
    • 23944503341 scopus 로고    scopus 로고
    • Datasets for evolutionary comparative genomics
    • Liberles DA: Datasets for evolutionary comparative genomics. Genome Biology 2005, 6:117.
    • (2005) Genome Biology , vol.6 , pp. 117
    • Liberles, D.A.1
  • 9
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura M: Evolutionary rate at the molecular level. Nature 1968, 217:624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 10
    • 27944474033 scopus 로고    scopus 로고
    • Selectionism and Neutralism in Molecular Evolution
    • Nei M: Selectionism and Neutralism in Molecular Evolution. Molecular Biology and Evolution 2005, 22:2318-2342.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 2318-2342
    • Nei, M.1
  • 12
    • 23944490117 scopus 로고    scopus 로고
    • Missense meanderings in sequence space: A biophysical view of protein evolution
    • DePristo MA, Weinreich DM, Hartl DL: Missense meanderings in sequence space: A biophysical view of protein evolution. Nature Reviews Genetics 2005, 6:678-687.
    • (2005) Nature Reviews Genetics , vol.6 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 13
    • 0036139093 scopus 로고    scopus 로고
    • Why are proteins marginally stable?
    • Taverna DM, Goldstein RA: Why are proteins marginally stable? Proteins 2002, 46:105-109.
    • (2002) Proteins , vol.46 , pp. 105-109
    • Taverna, D.M.1    Goldstein, R.A.2
  • 14
    • 0028064845 scopus 로고
    • Maximum - Likelihood phylogenetic estimation from DNA- sequences with variable rates over sites - Approximate methods
    • Yang Z: Maximum - likelihood phylogenetic estimation from DNA- sequences with variable rates over sites - Approximate methods. Journal of Molecular Evolution 1994, 309:306-314.
    • (1994) Journal of Molecular Evolution , vol.309 , pp. 306-314
    • Yang, Z.1
  • 16
    • 0344430832 scopus 로고    scopus 로고
    • Probabilism and phylogenetic inference
    • Siddall ME, Kluge AG: Probabilism and phylogenetic inference. Cladistics 1997, 13:313-336.
    • (1997) Cladistics , vol.13 , pp. 313-336
    • Siddall, M.E.1    Kluge, A.G.2
  • 17
    • 0034575442 scopus 로고    scopus 로고
    • Methods to detect selection in populations with applications to the human
    • Kreitman M: Methods to detect selection in populations with applications to the human. Annual Reviews of Genomics and Human Genetics 2000, 1:539-559.
    • (2000) Annual Reviews of Genomics and Human Genetics , vol.1 , pp. 539-559
    • Kreitman, M.1
  • 18
    • 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: tRNA gene number and codon usage in the C. elegans genome are co- adapted for optimal translation of highly expressed genes. Trends in Genetics 2000, 16:287-289.
    • (2000) Trends in Genetics , vol.16 , pp. 287-289
    • Duret, L.1
  • 19
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova M, Bielawski JP, Yang Z: Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Molecular Biology and Evolution 2001, 18:1585-1592.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 20
    • 0025939530 scopus 로고
    • Excess nonsynonymous substitution of shared polymorphic sites among self- incompatibility alleles of Solanaceae
    • Clark AG, Kao TH: Excess nonsynonymous substitution of shared polymorphic sites among self- incompatibility alleles of Solanaceae. Procedings of the National Academy of Sciences, USA 1991, 88:9823-9827.
    • (1991) Procedings of the National Academy of Sciences, USA , vol.88 , pp. 9823-9827
    • Clark, A.G.1    Kao, T.H.2
  • 21
    • 0030007094 scopus 로고    scopus 로고
    • Large- scale search for genes on which positive selection may operate
    • Endo T, Ikeo K, Gojobori T: Large- scale search for genes on which positive selection may operate. Molecular Biology and Evolution 1996, 13:685-690.
    • (1996) Molecular Biology and Evolution , vol.13 , pp. 685-690
    • Endo, T.1    Ikeo, K.2    Gojobori, T.3
  • 22
    • 0036840569 scopus 로고    scopus 로고
    • A sliding window - Based method to detect selective constraints in protein- coding genes and its application to RNA viruses
    • Fares MA, Elena SF, Ortiz J, Moya A, Barrio E: A sliding window - based method to detect selective constraints in protein- coding genes and its application to RNA viruses. Journal of Molecular Evolution 2002, 55:509-521.
    • (2002) Journal of Molecular Evolution , vol.55 , pp. 509-521
    • Fares, M.A.1    Elena, S.F.2    Ortiz, J.3    Moya, A.4    Barrio, E.5
  • 23
    • 8444220853 scopus 로고    scopus 로고
    • Three- dimensional window analysis for detecting positive selection at structural regions of proteins
    • Suzuki Y: Three- dimensional window analysis for detecting positive selection at structural regions of proteins. Molecular Biology and Evolution 2004, 21:2352-2359.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 2352-2359
    • Suzuki, Y.1
  • 25
    • 0842322358 scopus 로고    scopus 로고
    • Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: Functional and evolutionary implications
    • Kong H, Leebens-Mack J, Ni W, dePamphilis CW, Ma H: Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Molecular Biology and Evolution 2004, 21:117-128.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 117-128
    • Kong, H.1    Leebens-Mack, J.2    Ni, W.3    DePamphilis, C.W.4    Ma, H.5
  • 26
    • 0038414033 scopus 로고    scopus 로고
    • Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history
    • Clauss MJ, Mitchell-Olds T: Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history. Molecular Ecology 2003, 12:1287-1299.
    • (2003) Molecular Ecology , vol.12 , pp. 1287-1299
    • Clauss, M.J.1    Mitchell-Olds, T.2
  • 27
    • 1942485914 scopus 로고    scopus 로고
    • Functional divergence in tandemly duplicated Arabidopsis thaliana trypsin inhibitor genes
    • Clauss MJ, Mitchell-Olds T: Functional divergence in tandemly duplicated Arabidopsis thaliana trypsin inhibitor genes. Genetics 2004, 166:1419-1436.
    • (2004) Genetics , vol.166 , pp. 1419-1436
    • Clauss, M.J.1    Mitchell-Olds, T.2
  • 28
    • 0242497865 scopus 로고    scopus 로고
    • Evolutionary rate variation in anthocyanin pathway genes
    • Lu Y, Rausher MD: Evolutionary rate variation in anthocyanin pathway genes. Molecular Biology and Evolution 2003, 20:1844-1853.
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 1844-1853
    • Lu, Y.1    Rausher, M.D.2
  • 29
    • 1642503261 scopus 로고    scopus 로고
    • Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea)
    • Yang J, Gu H, Yang Z: Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). Journal of Molecular Evolution 2004, 58:54-63.
    • (2004) Journal of Molecular Evolution , vol.58 , pp. 54-63
    • Yang, J.1    Gu, H.2    Yang, Z.3
  • 30
    • 3843052542 scopus 로고    scopus 로고
    • Comparative evolutionary histories of chitinase genes in the Genus zea and Family poaceae
    • Tiffin P: Comparative evolutionary histories of chitinase genes in the Genus zea and Family poaceae. Genetics 2004, 167:1331-1340.
    • (2004) Genetics , vol.167 , pp. 1331-1340
    • Tiffin, P.1
  • 32
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 36
    • 14544306215 scopus 로고    scopus 로고
    • Molecular population genetics and the search for adaptive evolution in plants
    • Wright SI, Gaut BS: Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution 2005, 22:506-519.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 506-519
    • Wright, S.I.1    Gaut, B.S.2
  • 37
    • 0037296452 scopus 로고    scopus 로고
    • Selection on rapidly evolving proteins in the Arabidopsis genome
    • Barrier M, Bustamante CD, Yu J, Purugganan MD: Selection on rapidly evolving proteins in the Arabidopsis genome. Genetics 2003, 163:723-733.
    • (2003) Genetics , vol.163 , pp. 723-733
    • Barrier, M.1    Bustamante, C.D.2    Yu, J.3    Purugganan, M.D.4
  • 40
    • 0037366742 scopus 로고    scopus 로고
    • Comparative analysis of the self- incompatibility (S-) locusregion of Prunus mume: Identification of a pollen- expressed F-box gene with allelic diversity
    • Entani T, Iwano M, Shiba H, Che FS, Isogai A, Takayama S: Comparative analysis of the self- incompatibility (S-) locusregion of Prunus mume: identification of a pollen- expressed F-box gene with allelic diversity. Genes to Cells 2003, 8:203-213.
    • (2003) Genes to Cells , vol.8 , pp. 203-213
    • Entani, T.1    Iwano, M.2    Shiba, H.3    Che, F.S.4    Isogai, A.5    Takayama, S.6
  • 41
    • 0034094257 scopus 로고    scopus 로고
    • A rapid induction by elicitors of the mRNA encoding CCD- 1, a 14 kDa Ca2+ - Binding protein in wheat cultured cells
    • Takezawa D: A rapid induction by elicitors of the mRNA encoding CCD- 1, a 14 kDa Ca2+ - binding protein in wheat cultured cells. Plant Molecular Biology 2000, 42:807-817.
    • (2000) Plant Molecular Biology , vol.42 , pp. 807-817
    • Takezawa, D.1
  • 42
    • 0029339409 scopus 로고
    • Sequence and regulation of a late embryogenesis abundant group 3 protein of maize
    • White CN, Rivin CJ: Sequence and regulation of a late embryogenesis abundant group 3 protein of maize. Plant Physiology 1995, 108:1337-1338.
    • (1995) Plant Physiology , vol.108 , pp. 1337-1338
    • White, C.N.1    Rivin, C.J.2
  • 44
    • 0033767809 scopus 로고    scopus 로고
    • Differential screening indicates a dramatic change in mRNA profiles during grape berry ripening. Cloning and characterization of cDNAs encoding putative cell wall and stress response proteins
    • Davies C, Robinson SP: Differential screening indicates a dramatic change in mRNA profiles during grape berry ripening. Cloning and characterization of cDNAs encoding putative cell wall and stress response proteins. Plant Physiology 2000, 122:803-812.
    • (2000) Plant Physiology , vol.122 , pp. 803-812
    • Davies, C.1    Robinson, S.P.2
  • 50
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock DD, Taylor WR, Goldman N: Coevolving protein residues: Maximum likelihood identification and relationship to structure. Journal of Molecular Biology 1999, 287:187-198.
    • (1999) Journal of Molecular Biology , vol.287 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 52
    • 0029881442 scopus 로고    scopus 로고
    • Probabilistic reconstruction of ancestral protein sequences
    • Koshi JM, Goldstein RA: Probabilistic reconstruction of ancestral protein sequences. Journal of Molecular Evolution 1996, 42:313-320.
    • (1996) Journal of Molecular Evolution , vol.42 , pp. 313-320
    • Koshi, J.M.1    Goldstein, R.A.2
  • 56
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Lee C, Grasso C, Sharlow MF: Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18:452-64.
    • (2002) Bioinformatics , vol.18 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 57
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 59
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • Li WH, Wu CI, Luo CC: A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution 1985, 2:150-174.
    • (1985) Molecular Biology and Evolution , vol.2 , pp. 150-174
    • Li, W.H.1    Wu, C.I.2    Luo, C.C.3
  • 60
    • 0034748359 scopus 로고    scopus 로고
    • Evaluation of methods for determination of a reconstructed history of gene sequence evolution
    • Liberles DA: Evaluation of methods for determination of a reconstructed history of gene sequence evolution. Molecular Biology and Evolution 2001, 18:2040-2047.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 2040-2047
    • Liberles, D.A.1
  • 62
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Computational Applications in the Biological Sciences 1997, 13:555-556.
    • (1997) Computational Applications in the Biological Sciences , vol.13 , pp. 555-556
    • Yang, Z.1
  • 63
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
    • Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 64
    • 33644875286 scopus 로고    scopus 로고
    • The gene ontology (GO) project in 2006
    • Gene Ontology Consortium: The gene ontology (GO) project in 2006. Nucleic Acids Research 2006, 34:D322-D326.
    • (2006) Nucleic Acids Research , vol.34


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.