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Volumn 18, Issue 6, 2008, Pages 565-570

The evolution of plant genomes - scaling up from a population perspective

Author keywords

[No Author keywords available]

Indexed keywords

GENE DUPLICATION; GENETIC VARIABILITY; GENOME SIZE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PLANT GENOME; POLYPLOIDY; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL; REVIEW; SCALE UP; TRANSPOSON;

EID: 58549089667     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2008.11.005     Document Type: Review
Times cited : (23)

References (46)
  • 1
    • 0345306751 scopus 로고    scopus 로고
    • The origins of genome complexity
    • Lynch M., and Conery J.S. The origins of genome complexity. Science 302 (2003) 1401-1404
    • (2003) Science , vol.302 , pp. 1401-1404
    • Lynch, M.1    Conery, J.S.2
  • 2
    • 39749146549 scopus 로고    scopus 로고
    • Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis
    • Wright S.I., Nano N., Foxe J.P., and Dar V.N. Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis. Genet Res 90 (2008) 119-128
    • (2008) Genet Res , vol.90 , pp. 119-128
    • Wright, S.I.1    Nano, N.2    Foxe, J.P.3    Dar, V.N.4
  • 3
    • 34250709215 scopus 로고    scopus 로고
    • Sinauer. An extended discussion on the population genetic forces that can affect patterns of genome structure and evolution.
    • Lynch M. The Origins of Genome Architecture (2007), Sinauer. An extended discussion on the population genetic forces that can affect patterns of genome structure and evolution.
    • (2007) The Origins of Genome Architecture
    • Lynch, M.1
  • 4
    • 0037058932 scopus 로고    scopus 로고
    • Near-neutrality in evolution of genes and gene regulation
    • Ohta T. Near-neutrality in evolution of genes and gene regulation. Proc Natl Acad Sci U S A 99 (2002) 16134-16137
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 16134-16137
    • Ohta, T.1
  • 5
    • 34247214027 scopus 로고    scopus 로고
    • Impact of mating systems on patterns of sequence polymorphism in plants
    • A meta-analysis of available plant polymorphism sequence data that tested predictions about the effects of mating systems on molecular evolution.
    • Glemin S., Bazin E., and Charlesworth D. Impact of mating systems on patterns of sequence polymorphism in plants. Proc Royal Soc B 273 (2006) 3011-3019. A meta-analysis of available plant polymorphism sequence data that tested predictions about the effects of mating systems on molecular evolution.
    • (2006) Proc Royal Soc B , vol.273 , pp. 3011-3019
    • Glemin, S.1    Bazin, E.2    Charlesworth, D.3
  • 7
    • 34547108086 scopus 로고    scopus 로고
    • Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
    • The first comprehensive survey of nucleotide variation across the entire genome in a plant population.
    • Clark R.M., Schweikert G., Toomajian C., Ossowski S., Zeller G., Shinn P., Warthmann N., Hu T.T., Fu G., Hinds D.A., et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317 (2007) 338-342. The first comprehensive survey of nucleotide variation across the entire genome in a plant population.
    • (2007) Science , vol.317 , pp. 338-342
    • Clark, R.M.1    Schweikert, G.2    Toomajian, C.3    Ossowski, S.4    Zeller, G.5    Shinn, P.6    Warthmann, N.7    Hu, T.T.8    Fu, G.9    Hinds, D.A.10
  • 8
    • 0027305597 scopus 로고
    • The effects of deleterious mutations on neutral molecular variation
    • Charlesworth B., Morgan M.T., and Charlesworth D. The effects of deleterious mutations on neutral molecular variation. Genetics 134 (1993) 1289-1303
    • (1993) Genetics , vol.134 , pp. 1289-1303
    • Charlesworth, B.1    Morgan, M.T.2    Charlesworth, D.3
  • 9
    • 1842587751 scopus 로고    scopus 로고
    • Genome size: does bigger mean worse?
    • Charlesworth B., and Barton N. Genome size: does bigger mean worse?. Curr Biol 14 (2004) R233-R235
    • (2004) Curr Biol , vol.14
    • Charlesworth, B.1    Barton, N.2
  • 10
    • 1942520266 scopus 로고    scopus 로고
    • Testing genome complexity
    • Vinogradov A.E. Testing genome complexity. Science 304 (2004) 389-390
    • (2004) Science , vol.304 , pp. 389-390
    • Vinogradov, A.E.1
  • 11
    • 43549124770 scopus 로고    scopus 로고
    • Population size and genome size in fishes: a closer look
    • Gregory T.R., and Witt J.D.S. Population size and genome size in fishes: a closer look. Genome 51 (2008) 309-313
    • (2008) Genome , vol.51 , pp. 309-313
    • Gregory, T.R.1    Witt, J.D.S.2
  • 12
    • 0036729901 scopus 로고    scopus 로고
    • Rates and patterns of molecular evolution in inbred and outbred Arabidopsis
    • Wright S.I., Lauga B., and Charlesworth D. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol Biol Evol 19 (2002) 1407-1420
    • (2002) Mol Biol Evol , vol.19 , pp. 1407-1420
    • Wright, S.I.1    Lauga, B.2    Charlesworth, D.3
  • 13
    • 33845768012 scopus 로고    scopus 로고
    • Recombination: an underappreciated factor in the evolution of plant genomes
    • Gaut B.S., Wright S.I., Rizzon C., Dvorak J., and Anderson L.K. Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genetics 8 (2007) 77-84
    • (2007) Nat Rev Genetics , vol.8 , pp. 77-84
    • Gaut, B.S.1    Wright, S.I.2    Rizzon, C.3    Dvorak, J.4    Anderson, L.K.5
  • 14
    • 33751351656 scopus 로고    scopus 로고
    • Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata
    • Wright S.I., Foxe J.P., DeRose-Wilson L., Kawabe A., Looseley M., Gaut B.S., and Charlesworth D. Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics 174 (2006) 1421-1430
    • (2006) Genetics , vol.174 , pp. 1421-1430
    • Wright, S.I.1    Foxe, J.P.2    DeRose-Wilson, L.3    Kawabe, A.4    Looseley, M.5    Gaut, B.S.6    Charlesworth, D.7
  • 15
    • 45849116820 scopus 로고    scopus 로고
    • Selection on amino acid substitutions in Arabidopsis
    • First study to compare polymorphism and divergence data for a large number of genes from two closely related plant species.
    • Foxe J.P., Dar V.U.N., Zheng H., Nordborg M., Gaus B.S., and Wright S.I. Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol 25 (2008) 1375-1383. First study to compare polymorphism and divergence data for a large number of genes from two closely related plant species.
    • (2008) Mol Biol Evol , vol.25 , pp. 1375-1383
    • Foxe, J.P.1    Dar, V.U.N.2    Zheng, H.3    Nordborg, M.4    Gaus, B.S.5    Wright, S.I.6
  • 16
    • 44649164281 scopus 로고    scopus 로고
    • Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing
    • Cutter A.D., Wasmuth J.D., and Washington N.L. Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing. Genetics 178 (2008) 2093-2104
    • (2008) Genetics , vol.178 , pp. 2093-2104
    • Cutter, A.D.1    Wasmuth, J.D.2    Washington, N.L.3
  • 17
    • 35549007506 scopus 로고    scopus 로고
    • Mating systems and the efficacy of selection at the molecular level
    • Glemin S. Mating systems and the efficacy of selection at the molecular level. Genetics 177 (2007) 905-916
    • (2007) Genetics , vol.177 , pp. 905-916
    • Glemin, S.1
  • 18
    • 43049159700 scopus 로고    scopus 로고
    • Repeated big bangs and the expanding universe: directionality in plant genome size evolution
    • Hawkins J.S., Grover C.E., and Wendel J.F. Repeated big bangs and the expanding universe: directionality in plant genome size evolution. Plant Sci 174 (2008) 557-562
    • (2008) Plant Sci , vol.174 , pp. 557-562
    • Hawkins, J.S.1    Grover, C.E.2    Wendel, J.F.3
  • 19
    • 33750018038 scopus 로고    scopus 로고
    • Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation
    • Evidence of how retrotransposon activity increases after interspecific hybridization, leading to enlarged genomes in hybrid species.
    • Ungerer M.C., Strakosh S.C., and Zhen Y. Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Curr Biol 16 (2006) R872-R873. Evidence of how retrotransposon activity increases after interspecific hybridization, leading to enlarged genomes in hybrid species.
    • (2006) Curr Biol , vol.16
    • Ungerer, M.C.1    Strakosh, S.C.2    Zhen, Y.3
  • 20
    • 45849136671 scopus 로고    scopus 로고
    • A phylogenetic analysis of indel dynamics in the cotton genus
    • Grover C.E., Yu Y., Wing R.A., Paterson A.H., and Wendel J.F. A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol 25 (2008) 1415-1428
    • (2008) Mol Biol Evol , vol.25 , pp. 1415-1428
    • Grover, C.E.1    Yu, Y.2    Wing, R.A.3    Paterson, A.H.4    Wendel, J.F.5
  • 22
    • 33749392949 scopus 로고    scopus 로고
    • Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
    • Piegu B., Guyot R., Picault N., Roulin A., Saniyal A., Kim H., Collura K., Brar D.S., Jackson S., Wing R.A., and Panaud O. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16 (2006) 1262-1269
    • (2006) Genome Res , vol.16 , pp. 1262-1269
    • Piegu, B.1    Guyot, R.2    Picault, N.3    Roulin, A.4    Saniyal, A.5    Kim, H.6    Collura, K.7    Brar, D.S.8    Jackson, S.9    Wing, R.A.10    Panaud, O.11
  • 23
    • 40549120173 scopus 로고    scopus 로고
    • Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza
    • Roulin A., Piegu B., Wing R.A., and Panaud O. Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J 53 (2008) 950-959
    • (2008) Plant J , vol.53 , pp. 950-959
    • Roulin, A.1    Piegu, B.2    Wing, R.A.3    Panaud, O.4
  • 24
    • 33845878246 scopus 로고    scopus 로고
    • Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana
    • Nakamura Y., Itoh T., and Martin W. Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. Mol Biol Evol 24 (2007) 110-121
    • (2007) Mol Biol Evol , vol.24 , pp. 110-121
    • Nakamura, Y.1    Itoh, T.2    Martin, W.3
  • 25
    • 33845868781 scopus 로고    scopus 로고
    • Patterns of intron loss and gain in plants: intron-loss dominated evolution and genome-wide comparison of O. sativa and A. thaliana
    • Roy S.W., and Penny D. Patterns of intron loss and gain in plants: intron-loss dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol 24 (2007) 171-181
    • (2007) Mol Biol Evol , vol.24 , pp. 171-181
    • Roy, S.W.1    Penny, D.2
  • 27
    • 0033029164 scopus 로고    scopus 로고
    • Variation and divergence of death valley pupfish populations at retrotransposon-defined loci
    • Duvernell D.D., and Turner B.J. Variation and divergence of death valley pupfish populations at retrotransposon-defined loci. Mol Biol Evol 16 (1999) 363-371
    • (1999) Mol Biol Evol , vol.16 , pp. 363-371
    • Duvernell, D.D.1    Turner, B.J.2
  • 28
    • 0036250811 scopus 로고    scopus 로고
    • Alu repeats and human genomic diversity
    • Batzer M.A., and Deininger P.L. Alu repeats and human genomic diversity. Nat Rev Genetics 3 (2002) 370-379
    • (2002) Nat Rev Genetics , vol.3 , pp. 370-379
    • Batzer, M.A.1    Deininger, P.L.2
  • 29
    • 0024836563 scopus 로고
    • The population genetics of Drosophila transposable elements
    • Charlesworth B., and Langley C.H. The population genetics of Drosophila transposable elements. Annu Rev Genet 23 (1989) 251-287
    • (1989) Annu Rev Genet , vol.23 , pp. 251-287
    • Charlesworth, B.1    Langley, C.H.2
  • 30
    • 8444229706 scopus 로고    scopus 로고
    • Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies
    • Neafsey D.E., Blumenstiel J.P., and Hartl D. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Mol Biol Evol 21 (2004) 2310-2318
    • (2004) Mol Biol Evol , vol.21 , pp. 2310-2318
    • Neafsey, D.E.1    Blumenstiel, J.P.2    Hartl, D.3
  • 31
    • 0034924455 scopus 로고    scopus 로고
    • Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis
    • Wright S.I., Quang H.L., Schoen D.J., and Bureau T.E. Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis. Genetics 158 (2001) 1279-1288
    • (2001) Genetics , vol.158 , pp. 1279-1288
    • Wright, S.I.1    Quang, H.L.2    Schoen, D.J.3    Bureau, T.E.4
  • 32
    • 40849105280 scopus 로고    scopus 로고
    • Active miniature transposons from a plant genome and its nonrecombining Y chromosome
    • This study demonstrates that Y-linked MITEs segregate at substantially higher frequency than those found on autosomes consistent with a relaxation of purifying selection in nonrecombining regions.
    • Bergero R., and Charlesworth D. Active miniature transposons from a plant genome and its nonrecombining Y chromosome. Genetics 178 (2008) 1085-1092. This study demonstrates that Y-linked MITEs segregate at substantially higher frequency than those found on autosomes consistent with a relaxation of purifying selection in nonrecombining regions.
    • (2008) Genetics , vol.178 , pp. 1085-1092
    • Bergero, R.1    Charlesworth, D.2
  • 33
    • 0033288823 scopus 로고    scopus 로고
    • Sure facts, speculations, and open questions about the evolution of transposable element copy number
    • Nuzhdin S.V. Sure facts, speculations, and open questions about the evolution of transposable element copy number. Genetica 107 (1999) 129-137
    • (1999) Genetica , vol.107 , pp. 129-137
    • Nuzhdin, S.V.1
  • 34
    • 0033288975 scopus 로고    scopus 로고
    • Transposon dynamics and the breeding system
    • Wright S.I., and Schoen D.J. Transposon dynamics and the breeding system. Genetica 107 (1999) 139-148
    • (1999) Genetica , vol.107 , pp. 139-148
    • Wright, S.I.1    Schoen, D.J.2
  • 35
    • 0043026711 scopus 로고    scopus 로고
    • Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana
    • Wright S.I., Agrawal N., and Bureau T.E. Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res 13 (2003) 1897-1903
    • (2003) Genome Res , vol.13 , pp. 1897-1903
    • Wright, S.I.1    Agrawal, N.2    Bureau, T.E.3
  • 37
    • 35848941492 scopus 로고    scopus 로고
    • Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana
    • Hollister J.D., and Gaut B.S. Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana. Mol Biol Evol 24 (2008) 2515-2524
    • (2008) Mol Biol Evol , vol.24 , pp. 2515-2524
    • Hollister, J.D.1    Gaut, B.S.2
  • 39
    • 42549094998 scopus 로고    scopus 로고
    • Selection on major components of angiosperm genomes
    • Gaut B.S., and Ross-Ibarra. Selection on major components of angiosperm genomes. Science 320 (2008) 484-486
    • (2008) Science , vol.320 , pp. 484-486
    • Gaut, B.S.1    Ross-Ibarra2
  • 40
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force A., Lynch M., Pickett F.B., Amores A., Yan Y.L., and Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 (1999) 1531-1545
    • (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
  • 41
    • 30744464824 scopus 로고    scopus 로고
    • Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis
    • A systematic analysis of the fates of duplicated genes in a plant genome, demonstrating the evolution of subfunctionalization and neofunctionalization.
    • Duarte J.M., Cui L., Wall P.K., Zhang Q., Zhang X., Leebens-Mack J., Ma H., Altman N., and dePamphilis C.W. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol 23 (2006) 469-478. A systematic analysis of the fates of duplicated genes in a plant genome, demonstrating the evolution of subfunctionalization and neofunctionalization.
    • (2006) Mol Biol Evol , vol.23 , pp. 469-478
    • Duarte, J.M.1    Cui, L.2    Wall, P.K.3    Zhang, Q.4    Zhang, X.5    Leebens-Mack, J.6    Ma, H.7    Altman, N.8    dePamphilis, C.W.9
  • 42
    • 42549088178 scopus 로고    scopus 로고
    • Metabolic diversification - independent assembly of operon-like gene clusters in different plants
    • Field B., and Osbourn A.E. Metabolic diversification - independent assembly of operon-like gene clusters in different plants. Science 320 (2008) 543-547
    • (2008) Science , vol.320 , pp. 543-547
    • Field, B.1    Osbourn, A.E.2
  • 43
    • 33847634233 scopus 로고    scopus 로고
    • Evidence of interaction network evolution by whole genome duplications: a case study in MADS-box proteins
    • Veron A., Kaufmann K., and Borrnberg-Bauer E. Evidence of interaction network evolution by whole genome duplications: a case study in MADS-box proteins. Mol Biol Evol 24 (2007) 670-678
    • (2007) Mol Biol Evol , vol.24 , pp. 670-678
    • Veron, A.1    Kaufmann, K.2    Borrnberg-Bauer, E.3
  • 45
    • 52049107891 scopus 로고    scopus 로고
    • Contrasting patterns of transposable element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species
    • Hazzouri K.M., Mohajer A., Dejak S.I., Otto S.P., and Wright S.I. Contrasting patterns of transposable element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species. Genetics 179 (2008) 581-592
    • (2008) Genetics , vol.179 , pp. 581-592
    • Hazzouri, K.M.1    Mohajer, A.2    Dejak, S.I.3    Otto, S.P.4    Wright, S.I.5
  • 46
    • 43149114448 scopus 로고    scopus 로고
    • Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant
    • A large-scale survey of the expression patterns of duplicate genes following polyploidy genome formation.
    • Hovav R., Udall J.A., Chaudhary B., Rapp R., Flagel L., and Wendell J.F. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc Natl Acad Sci U S A 105 (2008) 6191-6195. A large-scale survey of the expression patterns of duplicate genes following polyploidy genome formation.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 6191-6195
    • Hovav, R.1    Udall, J.A.2    Chaudhary, B.3    Rapp, R.4    Flagel, L.5    Wendell, J.F.6


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