메뉴 건너뛰기




Volumn 8, Issue 8, 2007, Pages

Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: A novel strategy to estimate gene duplication rates

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; CATTLE; COMPUTER PROGRAM; CROSSING OVER; DOG; DROSOPHILA; GENE CONVERSION; GENE DUPLICATION; GENE REARRANGEMENT; GENETIC ANALYSIS; GENETIC CONSERVATION; HUMAN; HUMAN GENOME; MACACA; MATHEMATICAL ANALYSIS; MOLECULAR MECHANICS; MULTIGENE FAMILY; NONHUMAN; OPOSSUM; PHYLOGENY; QUANTITATIVE ANALYSIS; RETROPOSON; SPECIES DIFFERENCE; VERTEBRATE; YEAST; ANIMAL; DUPLICATE GENE; GENOME; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; MOUSE;

EID: 39749090675     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-8-r158     Document Type: Article
Times cited : (32)

References (48)
  • 2
    • 0037370306 scopus 로고    scopus 로고
    • Molecular evolution meets the genomics revolution
    • 10.1038/ng1088 12610535
    • Wolfe KH Li WH Molecular evolution meets the genomics revolution. Nat Genet 2003 33 255-265 10.1038/ng1088 12610535
    • (2003) Nat Genet , vol.33 , pp. 255-265
    • Wolfe, K.H.1    Li, W.H.2
  • 3
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • 10.1126/science.290.5494.1151 11073452
    • Lynch M Conery JS The evolutionary fate and consequences of duplicate genes. Science 2000 290 1151-1155 10.1126/science.290.5494.1151 11073452
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 4
    • 0036187351 scopus 로고    scopus 로고
    • Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
    • Gu Z Cavalcanti A Chen FC Bouman P Li WH Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 2000 19 256-262
    • (2000) Mol Biol Evol , vol.19 , pp. 256-262
    • Gu, Z.1    Cavalcanti, A.2    Chen, F.C.3    Bouman, P.4    Li, W.H.5
  • 5
    • 0035980032 scopus 로고    scopus 로고
    • Gene duplication and evolution
    • 10.1126/science.293.5535.1551a 11533445
    • Long M Thornton K Gene duplication and evolution. Science 2001 293 1551 10.1126/science.293.5535.1551a 11533445
    • (2001) Science , vol.293 , pp. 1551
    • Long, M.1    Thornton, K.2
  • 6
    • 0024591558 scopus 로고
    • On the rate of DNA sequence evolution in Drosophila
    • 10.1007/BF02603075 2501501
    • Sharp PM Li WH On the rate of DNA sequence evolution in Drosophila. J Mol Evol 1989 28 398-402 10.1007/BF02603075 2501501
    • (1989) J Mol Evol , vol.28 , pp. 398-402
    • Sharp, P.M.1    Li, W.H.2
  • 7
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: Non-neutral evolution at synonymous sites in mammals
    • 10.1038/nrg1770 16418745
    • Chamary JV Parmley JL Hurst LD Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 2006 7 98-108 10.1038/nrg1770 16418745
    • (2006) Nat Rev Genet , vol.7 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 8
    • 1942485886 scopus 로고    scopus 로고
    • The effect of gene conversion on the divergence between duplicated genes
    • 1470786 15082568 10.1534/genetics.166.3.1553
    • Teshima KM Innan H The effect of gene conversion on the divergence between duplicated genes. Genetics 2004 166 1553-1560 1470786 15082568 10.1534/genetics.166.3.1553
    • (2004) Genetics , vol.166 , pp. 1553-1560
    • Teshima, K.M.1    Innan, H.2
  • 9
    • 33646676990 scopus 로고    scopus 로고
    • Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat
    • 10.1093/molbev/msj093 16407460
    • Ezawa K OOta S Saitou N 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 2006 23 927-940 10.1093/ molbev/msj093 16407460
    • (2006) Mol Biol Evol , vol.23 , pp. 927-940
    • Ezawa, K.1    OOta, S.2    Saitou, N.3
  • 10
    • 8844244033 scopus 로고    scopus 로고
    • Very low gene duplication rate in the yeast genome
    • 10.1126/science.1102033 15550669
    • Gao LZ Innan H Very low gene duplication rate in the yeast genome. Science 2004 306 1367-1370 10.1126/science.1102033 15550669
    • (2004) Science , vol.306 , pp. 1367-1370
    • Gao, L.Z.1    Innan, H.2
  • 11
    • 0037500141 scopus 로고    scopus 로고
    • Evolution by gene duplication: An update
    • 10.1016/S0169-5347(03)00033-8
    • Zhang J Evolution by gene duplication: An update. Trends Ecology Evol 2003 18 292-298 10.1016/S0169-5347(03)00033-8
    • (2003) Trends Ecology Evol , vol.18 , pp. 292-298
    • Zhang, J.1
  • 12
    • 0027284770 scopus 로고
    • Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse
    • 10.1006/geno.1993.1133 8486346
    • Lundin LG Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 1993 16 1-19 10.1006/geno.1993.1133 8486346
    • (1993) Genomics , vol.16 , pp. 1-19
    • Lundin, L.G.1
  • 13
    • 0030473920 scopus 로고    scopus 로고
    • Genome duplications in the evolution of early vertebrates
    • 10.1016/S0959-437X(96)80026-8 8994842
    • Sidow A Genome duplications in the evolution of early vertebrates. Curr Opin Genet Dev 1996 6 715-722 10.1016/S0959-437X(96)80026-8 8994842
    • (1996) Curr Opin Genet Dev , vol.6 , pp. 715-722
    • Sidow, A.1
  • 14
    • 0032733930 scopus 로고    scopus 로고
    • Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions
    • 10.1016/S0955-0674(99)00039-3 10600714
    • Meyer A Schartl M Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 1999 11 699-704 10.1016/ S0955-0674(99)00039-3 10600714
    • (1999) Curr Opin Cell Biol , vol.11 , pp. 699-704
    • Meyer, A.1    Schartl, M.2
  • 15
    • 0035179702 scopus 로고    scopus 로고
    • Pattern and timing of gene duplication in animal genomes
    • 311158 11691848 10.1101/gr.155801
    • Friedman R Hughes AL Pattern and timing of gene duplication in animal genomes. Genome Res 2001 11 1842-1847 311158 11691848 10.1101/gr.155801
    • (2001) Genome Res , vol.11 , pp. 1842-1847
    • Friedman, R.1    Hughes, A.L.2
  • 16
    • 0035010738 scopus 로고    scopus 로고
    • Ancient genome duplications did not structure the human Hox-bearing chromosomes
    • 311105 11337473 10.1101/gr.GR-1600R
    • Hughes AL da Silva J Friedman R Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res 2001 11 771-780 311105 11337473 10.1101/gr.GR-1600R
    • (2001) Genome Res , vol.11 , pp. 771-780
    • Hughes, A.L.1    da Silva, J.2    Friedman, R.3
  • 17
    • 0037227485 scopus 로고    scopus 로고
    • The temporal distribution of gene duplication events in a set of highly conserved human gene families
    • 10.1093/molbev/msg017 12519918
    • Friedman R Hughes AL The temporal distribution of gene duplication events in a set of highly conserved human gene families. Mol Biol Evol 2003 20 154-161 10.1093/molbev/msg017 12519918
    • (2003) Mol Biol Evol , vol.20 , pp. 154-161
    • Friedman, R.1    Hughes, A.L.2
  • 18
    • 2442715046 scopus 로고    scopus 로고
    • Two patterns of genome organization in mammals: The chromosomal distribution of duplicate genes in human and mouse
    • 10.1093/molbev/msh076 14963098
    • Friedman R Hughes AL Two patterns of genome organization in mammals: The chromosomal distribution of duplicate genes in human and mouse. Mol Biol Evol 2004 21 1008-1013 10.1093/molbev/msh076 14963098
    • (2004) Mol Biol Evol , vol.21 , pp. 1008-1013
    • Friedman, R.1    Hughes, A.L.2
  • 19
    • 33749563310 scopus 로고    scopus 로고
    • A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat
    • 10.1093/molbev/msl085 16901985
    • Shoja V Zhang L A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat. Mol Biol Evol 2006 23 2134-2141 10.1093/molbev/ msl085 16901985
    • (2006) Mol Biol Evol , vol.23 , pp. 2134-2141
    • Shoja, V.1    Zhang, L.2
  • 20
    • 0029035295 scopus 로고
    • Tandem genes and clustered genes
    • 10.1006/jtbi.1995.0122 7564393
    • Graham G Tandem genes and clustered genes. J Theor Biol 1995 175 71-87 10.1006/jtbi.1995.0122 7564393
    • (1995) J Theor Biol , vol.175 , pp. 71-87
    • Graham, G.1
  • 21
    • 0025864962 scopus 로고
    • Retroposons: Seeds of evolution
    • 10.1126/science.1990437 1990437
    • Brosius J Retroposons: Seeds of evolution. Science 1991 251 753 10.1126/ science.1990437 1990437
    • (1991) Science , vol.251 , pp. 753
    • Brosius, J.1
  • 22
    • 1542513556 scopus 로고    scopus 로고
    • Mobile elements: Drivers of genome evolution
    • 10.1126/science.1089670 15016989
    • Kazazian HH Jr Mobile elements: Drivers of genome evolution. Science 2004 303 1626-1632 10.1126/science.1089670 15016989
    • (2004) Science , vol.303 , pp. 1626-1632
    • Kazazian Jr., H.H.1
  • 23
    • 0036906987 scopus 로고    scopus 로고
    • Retroposed new genes out of the X in Drosophila
    • 187566 12466289 10.1101/gr.6049
    • Betran E Thornton K Long M Retroposed new genes out of the X in Drosophila. Genome Res 2002 12 1854-1859 187566 12466289 10.1101/gr.6049
    • (2002) Genome Res , vol.12 , pp. 1854-1859
    • Betran, E.1    Thornton, K.2    Long, M.3
  • 24
    • 0242354129 scopus 로고    scopus 로고
    • The origin of new genes: Glimpses from the young and old
    • 10.1038/nrg1204 14634634
    • Long M Betran E Thornton K Wang W The origin of new genes: Glimpses from the young and old. Nat Rev Genet 2003 4 865-875 10.1038/nrg1204 14634634
    • (2003) Nat Rev Genet , vol.4 , pp. 865-875
    • Long, M.1    Betran, E.2    Thornton, K.3    Wang, W.4
  • 25
    • 1642475221 scopus 로고    scopus 로고
    • Extensive gene traffic on the mammalian X chromosome
    • 10.1126/science.1090042 14739461
    • Emerson JJ Kaessmann H Betran E Long M Extensive gene traffic on the mammalian X chromosome. Science 2004 303 537-540 10.1126/science.1090042 14739461
    • (2004) Science , vol.303 , pp. 537-540
    • Emerson, J.J.1    Kaessmann, H.2    Betran, E.3    Long, M.4
  • 26
    • 27844557002 scopus 로고    scopus 로고
    • Emergence of young human genes after a burst of retroposition in primates
    • 1251493 16201836 10.1371/journal.pbio.0030357
    • Marques AC Dupanloup I Vinckenbosch N Reymond A Kaessmann H Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 2005 3 e357 1251493 16201836 10.1371/journal.pbio.0030357
    • (2005) PLoS Biol , vol.3
    • Marques, A.C.1    Dupanloup, I.2    Vinckenbosch, N.3    Reymond, A.4    Kaessmann, H.5
  • 27
    • 33747465505 scopus 로고    scopus 로고
    • High rate of chimeric gene origination by retroposition in plant genomes
    • 1533979 16829590 10.1105/tpc.106.041905
    • Wang W Zheng H Fan C Li J Shi J Cai Z Zhang G Liu D Zhang J Vang S High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 2006 18 1791-1802 1533979 16829590 10.1105/tpc.106.041905
    • (2006) Plant Cell , vol.18 , pp. 1791-1802
    • Wang, W.1    Zheng, H.2    Fan, C.3    Li, J.4    Shi, J.5    Cai, Z.6    Zhang, G.7    Liu, D.8    Zhang, J.9    Vang, S.10
  • 28
    • 33644777605 scopus 로고    scopus 로고
    • Evolutionary fate of retroposed gene copies in the human genome
    • 1413932 16492757 10.1073/pnas.0511307103
    • Vinckenbosch N Dupanloup I Kaessmann H Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 2006 103 3220-3225 1413932 16492757 10.1073/pnas.0511307103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 3220-3225
    • Vinckenbosch, N.1    Dupanloup, I.2    Kaessmann, H.3
  • 29
    • 34147128526 scopus 로고    scopus 로고
    • Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila
    • 1839131 17233920 10.1186/gb-2007-8-1-r11
    • Bai Y Casola C Feschotte C Betran E Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol 2007 8 R11 1839131 17233920 10.1186/gb-2007-8-1-r11
    • (2007) Genome Biol , vol.8
    • Bai, Y.1    Casola, C.2    Feschotte, C.3    Betran, E.4
  • 30
    • 17144473540 scopus 로고    scopus 로고
    • Are we polyploids? A brief history of one hypothesis
    • 10.1101/gr.188801 11337465
    • Makalowski W Are we polyploids? A brief history of one hypothesis. Genome Res 2001 11 667-670 10.1101/gr.188801 11337465
    • (2001) Genome Res , vol.11 , pp. 667-670
    • Makalowski, W.1
  • 31
    • 2442680252 scopus 로고    scopus 로고
    • Analysis of segmental duplications and genome assembly in the mouse
    • 479105 15123579 10.1101/gr.2238404
    • Bailey JA Church DM Ventura M Rocchi M Eichler EE Analysis of segmental duplications and genome assembly in the mouse. Genome Res 2004 14 789-801 479105 15123579 10.1101/gr.2238404
    • (2004) Genome Res , vol.14 , pp. 789-801
    • Bailey, J.A.1    Church, D.M.2    Ventura, M.3    Rocchi, M.4    Eichler, E.E.5
  • 33
    • 10344222632 scopus 로고    scopus 로고
    • Patterns of segmental duplication in the human genome
    • 10.1093/molbev/msh262 15371527
    • Zhang L Lu HH Chung WY Yang J Li WH Patterns of segmental duplication in the human genome. Mol Biol Evol 2005 22 135-141 10.1093/molbev/msh262 15371527
    • (2005) Mol Biol Evol , vol.22 , pp. 135-141
    • Zhang, L.1    Lu, H.H.2    Chung, W.Y.3    Yang, J.4    Li, W.H.5
  • 34
    • 15244356879 scopus 로고    scopus 로고
    • Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee
    • 554819 15728731 10.1073/pnas.0500436102
    • Lu J Wu CI Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci USA 2005 102 4063-4067 554819 15728731 10.1073/pnas.0500436102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4063-4067
    • Lu, J.1    Wu, C.I.2
  • 35
    • 20644465818 scopus 로고    scopus 로고
    • A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate
    • 10.1016/j.tig.2005.05.005 15946765
    • Wyckoff GJ Malcom CM Vallender EJ Lahn BT A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. Trends Genet 2005 21 381-385 10.1016/j.tig.2005.05.005 15946765
    • (2005) Trends Genet , vol.21 , pp. 381-385
    • Wyckoff, G.J.1    Malcom, C.M.2    Vallender, E.J.3    Lahn, B.T.4
  • 36
    • 0036897666 scopus 로고    scopus 로고
    • Slow molecular clocks in Old World monkeys, apes, and humans
    • 12446810
    • Yi S Ellsworth D Li W Slow molecular clocks in Old World monkeys, apes, and humans. Mol Biol Evol 2002 19 2191-2198 12446810
    • (2002) Mol Biol Evol , vol.19 , pp. 2191-2198
    • Yi, S.1    Ellsworth, D.2    Li, W.3
  • 37
    • 33144464980 scopus 로고    scopus 로고
    • Role of positive selection in the retention of duplicate genes in mammalian genomes
    • 1413713 16461903 10.1073/pnas.0510388103
    • Shiu SH Byrnes JK Pan R Zhang P Li WH Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci USA 2006 103 2232-2236 1413713 16461903 10.1073/pnas.0510388103
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 2232-2236
    • Shiu, S.H.1    Byrnes, J.K.2    Pan, R.3    Zhang, P.4    Li, W.H.5
  • 38
    • 0142059650 scopus 로고    scopus 로고
    • An Alu transposition model for the origin and expansion of human segmental duplications
    • 1180605 14505274 10.1086/378594
    • Bailey JA Liu G Eichler EE An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 2003 73 823-834 1180605 14505274 10.1086/378594
    • (2003) Am J Hum Genet , vol.73 , pp. 823-834
    • Bailey, J.A.1    Liu, G.2    Eichler, E.E.3
  • 39
    • 0030076124 scopus 로고    scopus 로고
    • Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis
    • 10.1006/mpev.1996.0012 8673286
    • Li WH Ellsworth DL Krushkal J Chang BH Hewett-Emmett D Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol Phylogenet Evol 1996 5 182-187 10.1006/ mpev.1996.0012 8673286
    • (1996) Mol Phylogenet Evol , vol.5 , pp. 182-187
    • Li, W.H.1    Ellsworth, D.L.2    Krushkal, J.3    Chang, B.H.4    Hewett-Emmett, D.5
  • 42
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • 1460548 10101175
    • Force A Lynch M Pickett FB Amores A Yan YL Postlethwait J Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999 151 1531-1545 1460548 10101175
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3    Amores, A.4    Yan, Y.L.5    Postlethwait, J.6
  • 43
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 308517 7984417 10.1093/nar/22.22.4673
    • Thompson J Higgins D Gibson T CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994 22 4673-4680 308517 7984417 10.1093/nar/22.22.4673
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.1    Higgins, D.2    Gibson, T.3
  • 44
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • 9367129
    • Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997 13 555-556 9367129
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 45
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • 10666704
    • Yang Z Nielsen R Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000 17 32-43 10666704
    • (2000) Mol Biol Evol , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 46
    • 33748324384 scopus 로고    scopus 로고
    • R Development Core Team Vienna, Austria: R Foundation for Statistical Computing
    • R Development Core Team R: A Language and Environment for Statistical Computing Vienna, Austria: R Foundation for Statistical Computing 2006
    • (2006) R: A Language and Environment for Statistical Computing
  • 47
    • 33845982198 scopus 로고    scopus 로고
    • Characterization of intron loss events in mammals
    • 1716263 17108319 10.1101/gr.5703406
    • Coulombe-Huntington J Majewski J Characterization of intron loss events in mammals. Genome Res 2007 17 23-32 1716263 17108319 10.1101/gr.5703406
    • (2007) Genome Res , vol.17 , pp. 23-32
    • Coulombe-Huntington, J.1    Majewski, J.2
  • 48
    • 18944377637 scopus 로고    scopus 로고
    • The Caml Language
    • The Caml Language http://caml.inria.fr


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.