메뉴 건너뛰기




Volumn 177, Issue 3, 2007, Pages 1753-1763

Extensive concerted evolution of rice paralogs and the road to regaining independence

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE CONVERSION; GENE DUPLICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; MOLECULAR EVOLUTION; PARALOGY; PLANT CHROMOSOME; PLANT GENETICS; POLYPLOIDY; PRIORITY JOURNAL; RICE; SEQUENCE ANALYSIS; SORGHUM; SPECIES DIFFERENCE;

EID: 37249045857     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.073197     Document Type: Article
Times cited : (84)

References (46)
  • 2
    • 0041746470 scopus 로고
    • Chromosome numbers, patterns of distribution, and apomixis in Antennaria (Asteraceae: Inuleae)
    • BAYER, R. J., and G. L. STEBBINS, 1987 Chromosome numbers, patterns of distribution, and apomixis in Antennaria (Asteraceae: Inuleae). Syst. Bot. 12: 305-319.
    • (1987) Syst. Bot , vol.12 , pp. 305-319
    • BAYER, R.J.1    STEBBINS, G.L.2
  • 3
    • 0036218945 scopus 로고    scopus 로고
    • Rapid concerted evolution via gene conversion at the Drosophila hsp70 genes
    • BETTENCOURT, B. R., and M. E. FEDER, 2002 Rapid concerted evolution via gene conversion at the Drosophila hsp70 genes. J. Mol. Evol. 54: 569-586.
    • (2002) J. Mol. Evol , vol.54 , pp. 569-586
    • BETTENCOURT, B.R.1    FEDER, M.E.2
  • 5
    • 33644499450 scopus 로고    scopus 로고
    • Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication
    • CHAPMAN, B. A., J. E. BOWERS, F. A. FELTUS and A. H. PATERSON, 2006 Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc. Natl. Acad. Sci. USA 103: 2730-2735.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 2730-2735
    • CHAPMAN, B.A.1    BOWERS, J.E.2    FELTUS, F.A.3    PATERSON, A.H.4
  • 6
    • 0033452727 scopus 로고    scopus 로고
    • Duplicated genes evolve independently after polyploid formation in cotton
    • CRONN, R. C., R. L. SMALL and J. F. WENDEL, 1999 Duplicated genes evolve independently after polyploid formation in cotton. Proc. Natl. Acad. Sci. USA 96: 14406-14411.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 14406-14411
    • CRONN, R.C.1    SMALL, R.L.2    WENDEL, J.F.3
  • 7
    • 33646676990 scopus 로고    scopus 로고
    • Genome-wide search of gene conversions in duplicated genes of mouse and rat
    • 2006 Proceedings of the SMBE Tri-National Young Investigators' Workshop
    • EZAWA, K., S. OOTA and N. SAITOU, 2006 Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat. Mol. Biol. Evol. 23: 927-940.
    • (2005) Mol. Biol. Evol , vol.23 , pp. 927-940
    • EZAWA, K.1    OOTA, S.2    SAITOU, N.3
  • 8
    • 0037303814 scopus 로고    scopus 로고
    • Gene conversion drives GC content evolution in mammalian histones
    • GALTIER, N., 2003 Gene conversion drives GC content evolution in mammalian histones. Trends Genet. 19: 65-68.
    • (2003) Trends Genet , vol.19 , pp. 65-68
    • GALTIER, N.1
  • 9
    • 8844244033 scopus 로고    scopus 로고
    • Very low gene duplication rate in the yeast genome
    • GAO, L. Z., and H. INNAN, 2004 Very low gene duplication rate in the yeast genome. Science 306: 1367-1370.
    • (2004) Science , vol.306 , pp. 1367-1370
    • GAO, L.Z.1    INNAN, H.2
  • 10
    • 0013977819 scopus 로고
    • Studies on mitotic gene conversion in Ustilago
    • HOLLIDAY, R., 1966 Studies on mitotic gene conversion in Ustilago. Genet. Res. 8: 323-337.
    • (1966) Genet. Res , vol.8 , pp. 323-337
    • HOLLIDAY, R.1
  • 11
    • 0027423610 scopus 로고
    • Evolution of genes in a tetraploid animal, Xenopus laevis
    • HUGHES, M. K., and A. L. HUGHES, 1993 Evolution of genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10: 1360-1369.
    • (1993) Mol. Biol. Evol , vol.10 , pp. 1360-1369
    • HUGHES, M.K.1    HUGHES, A.L.2
  • 13
    • 33846857991 scopus 로고    scopus 로고
    • Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
    • ITOH, T., T. TANAKA, R. A. BARRERO, C. YAMASAKI, Y. FUJII et al., 2007 Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17: 175-183.
    • (2007) Genome Res , vol.17 , pp. 175-183
    • ITOH, T.1    TANAKA, T.2    BARRERO, R.A.3    YAMASAKI, C.4    FUJII, Y.5
  • 14
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    • KELLIS, M., B. W. BIRREN and E. S. LANDER, 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
  • 16
    • 85007912102 scopus 로고
    • The secondary association of chromosomes
    • LAWRENCE, W. J. C., 1931 The secondary association of chromosomes. Cytologia 2: 352-384.
    • (1931) Cytologia , vol.2 , pp. 352-384
    • LAWRENCE, W.J.C.1
  • 17
    • 33644757635 scopus 로고    scopus 로고
    • The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis
    • LI, L., M. JEAN and F. BELZILE, 2006 The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis. Plant J. 45: 908-916.
    • (2006) Plant J , vol.45 , pp. 908-916
    • LI, L.1    JEAN, M.2    BELZILE, F.3
  • 18
    • 0033759525 scopus 로고    scopus 로고
    • Gene conversion drives within genic sequences: Concerted evolution of ribosomal RNA genes in bacteria and archaea
    • LIAO, D., 2000 Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. J. Mol. Evol. 51: 305-317.
    • (2000) J. Mol. Evol , vol.51 , pp. 305-317
    • LIAO, D.1
  • 19
    • 33749261964 scopus 로고    scopus 로고
    • Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes
    • LIN, Y. S., J. K. BYRNES, J.K. HWANG and W. H. LI, 2006 Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc. Natl. Acad. Sci. USA 103: 14412-14416.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 14412-14416
    • LIN, Y.S.1    BYRNES, J.K.2    HWANG, J.K.3    LI, W.H.4
  • 20
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • LYNCH, M., and J. S. CONERY, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • LYNCH, M.1    CONERY, J.S.2
  • 21
    • 0035697435 scopus 로고    scopus 로고
    • LYNCH, M., M. O'HELY, B. WALSH and A. FORCE, 2001 The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
    • LYNCH, M., M. O'HELY, B. WALSH and A. FORCE, 2001 The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
  • 22
    • 27844526579 scopus 로고    scopus 로고
    • Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana
    • MONDRAGON-PALOMINO, M., and B. S. GAUT, 2005 Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol. Biol. Evol. 22: 2444-2456.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 2444-2456
    • MONDRAGON-PALOMINO, M.1    GAUT, B.S.2
  • 23
    • 0347364640 scopus 로고    scopus 로고
    • The early stages of duplicate gene evolution
    • MOORE, R. C., and M. D. PURUGGANAN, 2003 The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. USA 100: 15682-15687.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15682-15687
    • MOORE, R.C.1    PURUGGANAN, M.D.2
  • 24
    • 0001224667 scopus 로고
    • Some genetic aspects of sex
    • MULLER, H. J., 1932 Some genetic aspects of sex. Am. Nat. 66: 118-138.
    • (1932) Am. Nat , vol.66 , pp. 118-138
    • MULLER, H.J.1
  • 25
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • NEI, M., and T. GOJOBORI, 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
    • (1986) Mol. Biol. Evol , vol.3 , pp. 418-426
    • NEI, M.1    GOJOBORI, T.2
  • 27
    • 0021362937 scopus 로고
    • Some models of gene conversion for treating the evolution of multigene families
    • OHTA, T., 1984 Some models of gene conversion for treating the evolution of multigene families. Genetics 106: 517-528.
    • (1984) Genetics , vol.106 , pp. 517-528
    • OHTA, T.1
  • 28
    • 0038306149 scopus 로고    scopus 로고
    • Evolution by gene duplication revisited: Differentiation of regulatory elements versus proteins
    • OHTA, T., 2003 Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins. Genetica 118: 209-216.
    • (2003) Genetica , vol.118 , pp. 209-216
    • OHTA, T.1
  • 29
    • 3042836334 scopus 로고    scopus 로고
    • Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
    • PATERSON, A. H., J. E. BOWERS and B. A. CHAPMAN, 2004 Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA 101: 9903-9908.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 9903-9908
    • PATERSON, A.H.1    BOWERS, J.E.2    CHAPMAN, B.A.3
  • 30
    • 33750173564 scopus 로고    scopus 로고
    • Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
    • PATERSON, A. H., B. A. CHAPMAN, J. C. KISSINGER, J. E. BOWERS, F. A. FELTUS et al., 2006 Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet. 22: 597-602.
    • (2006) Trends Genet , vol.22 , pp. 597-602
    • PATERSON, A.H.1    CHAPMAN, B.A.2    KISSINGER, J.C.3    BOWERS, J.E.4    FELTUS, F.A.5
  • 31
    • 37249092163 scopus 로고    scopus 로고
    • PETES, T. D., R. E. MALONE and L. S. SYMINGTON, 1991 Recombination in yeast, pp. 407-421 in The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by J. Broach, E. Jones and J. Pringle. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • PETES, T. D., R. E. MALONE and L. S. SYMINGTON, 1991 Recombination in yeast, pp. 407-421 in The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by J. Broach, E. Jones and J. Pringle. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • 32
    • 27544478621 scopus 로고    scopus 로고
    • RICE CHROMOSOMES 11 and 12 SEQUENCING CONSORTIA, 2005 The sequence of rice chromosomes 11 and 12, rice in disease resistance genes and recent gene duplications. BMC Biology 3: 20.
    • RICE CHROMOSOMES 11 and 12 SEQUENCING CONSORTIA, 2005 The sequence of rice chromosomes 11 and 12, rice in disease resistance genes and recent gene duplications. BMC Biology 3: 20.
  • 33
    • 0024356449 scopus 로고
    • Statistical tests for detecting gene conversion
    • SAWYER, S., 1989 Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6: 526-538.
    • (1989) Mol. Biol. Evol , vol.6 , pp. 526-538
    • SAWYER, S.1
  • 34
    • 0032953158 scopus 로고    scopus 로고
    • Gene duplication and gene conversion in the Caenorhabditis elegans genome
    • SEMPLE, C., and K. H. WOLFE, 1999 Gene duplication and gene conversion in the Caenorhabditis elegans genome. J. Mol. Evol. 48: 555-564.
    • (1999) J. Mol. Evol , vol.48 , pp. 555-564
    • SEMPLE, C.1    WOLFE, K.H.2
  • 35
    • 0037967242 scopus 로고    scopus 로고
    • The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
    • SKALETSKY, H., T. KURODA-KAWAGUCHI, P. J. MINX, H. S. CORDUM, L. HILLIER et al., 2003 The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423: 825-837.
    • (2003) Nature , vol.423 , pp. 825-837
    • SKALETSKY, H.1    KURODA-KAWAGUCHI, T.2    MINX, P.J.3    CORDUM, H.S.4    HILLIER, L.5
  • 36
    • 0000032326 scopus 로고
    • Possible significance of duplications in evolution
    • STEPHENS, S., 1951 Possible significance of duplications in evolution. Adv. Genet. 4: 247-265.
    • (1951) Adv. Genet , vol.4 , pp. 247-265
    • STEPHENS, S.1
  • 37
    • 0018869075 scopus 로고
    • Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae
    • SZOSTAK, J. W., and R. WU, 1980 Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284: 426-430.
    • (1980) Nature , vol.284 , pp. 426-430
    • SZOSTAK, J.W.1    WU, R.2
  • 38
    • 10944230777 scopus 로고    scopus 로고
    • Duplication and divergence: The evolution of new genes and old ideas
    • TAYLOR, J. S., and J. RAES, 2004 Duplication and divergence: the evolution of new genes and old ideas. Ann. Rev. Genet. 38: 615-643.
    • (2004) Ann. Rev. Genet , vol.38 , pp. 615-643
    • TAYLOR, J.S.1    RAES, J.2
  • 39
    • 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., D. G. HIGGINS and T. J. GIBSON, 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.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • THOMPSON, J.D.1    HIGGINS, D.G.2    GIBSON, T.J.3
  • 40
    • 21144453167 scopus 로고    scopus 로고
    • Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization
    • TOCCHINI-VALENTINI, G. D., P. FRUSCOLONI and G. P. TOCCHINI-VALENTINI, 2005 Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc. Natl. Acad. Sci. USA 102: 8933-8938.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 8933-8938
    • TOCCHINI-VALENTINI, G.D.1    FRUSCOLONI, P.2    TOCCHINI-VALENTINI, G.P.3
  • 41
    • 14244250895 scopus 로고    scopus 로고
    • Duplication and DNA segmental loss in the rice genome: Implications for diploidization
    • WANG, X., X. SHI, B. HAO, S. GE and J. LUO, 2005 Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165: 937-946.
    • (2005) New Phytol , vol.165 , pp. 937-946
    • WANG, X.1    SHI, X.2    HAO, B.3    GE, S.4    LUO, J.5
  • 42
    • 33750489449 scopus 로고    scopus 로고
    • Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
    • WANG, X., X. SHI, Z. LI, Q. ZHU, L. KONG et al., 2006 Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics 7: 447.
    • (2006) BMC Bioinformatics , vol.7 , pp. 447
    • WANG, X.1    SHI, X.2    LI, Z.3    ZHU, Q.4    KONG, L.5
  • 43
    • 0033938481 scopus 로고    scopus 로고
    • Gene conversions may obscure actin gene family relationships
    • WHITE, M. E., and B. I. CROTHER, 2000 Gene conversions may obscure actin gene family relationships. J. Mol. Evol. 50: 170-174.
    • (2000) J. Mol. Evol , vol.50 , pp. 170-174
    • WHITE, M.E.1    CROTHER, B.I.2
  • 44
    • 20144366003 scopus 로고    scopus 로고
    • The genomes of Oryza sativa: A history of duplications
    • YU, J., J. WANG, W. LIN, S. LI, H. LI et al., 2005 The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3: e38.
    • (2005) PLoS Biol , vol.3
    • YU, J.1    WANG, J.2    LIN, W.3    LI, S.4    LI, H.5
  • 45
    • 0036726239 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana
    • ZHANG, L., T. J. VISION and B. S. GAUT, 2002 Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19(9): 1464-1473.
    • (2002) Mol. Biol. Evol , vol.19 , Issue.9 , pp. 1464-1473
    • ZHANG, L.1    VISION, T.J.2    GAUT, B.S.3
  • 46
    • 21244501403 scopus 로고    scopus 로고
    • Phylogenetic relationships among Agenome species of the genus Oryza revealed by intron sequences of four nuclear genes
    • ZHU, Q., and S. GE, 2005 Phylogenetic relationships among Agenome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 167: 249-265.
    • (2005) New Phytol , vol.167 , pp. 249-265
    • ZHU, Q.1    GE, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.