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Volumn 7, Issue 3, 2012, Pages

Transposable elements are a major cause of somatic polymorphism in vitis vinifera L.

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; CONTROLLED STUDY; CULTIVAR; GENE IDENTIFICATION; GENE INSERTION; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GRAPE; INDEL MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PLANT GENOME; QUANTITATIVE STUDY; RAMET; SEQUENCE HOMOLOGY; SOMATIC MUTATION; STRAIN DIFFERENCE; TRANSPOSON; CLONING; DNA SEQUENCE; GENETICS; LONG TERMINAL REPEAT; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; VITIS;

EID: 84858118265     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032973     Document Type: Article
Times cited : (81)

References (57)
  • 1
    • 0021715393 scopus 로고
    • Significance of responses of the genome to challenge
    • McClintock B, (1984) Significance of responses of the genome to challenge. Science 226: 792-801.
    • (1984) Science , vol.226 , pp. 792-801
    • McClintock, B.1
  • 2
    • 50449091647 scopus 로고    scopus 로고
    • Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease
    • McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, et al. (2008) Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 40: 1107-1112.
    • (2008) Nat Genet , vol.40 , pp. 1107-1112
    • McCarroll, S.A.1    Huett, A.2    Kuballa, P.3    Chilewski, S.D.4    Landry, A.5
  • 4
    • 33745434299 scopus 로고    scopus 로고
    • Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes
    • McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, et al. (2006) Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol 141: 26-31.
    • (2006) Plant Physiol , vol.141 , pp. 26-31
    • McNally, K.L.1    Bruskiewich, R.2    Mackill, D.3    Buell, C.R.4    Leach, J.E.5
  • 5
    • 1542513556 scopus 로고    scopus 로고
    • Mobile Elements: Drivers of Genome Evolution
    • Kazazian HH, (2004) Mobile Elements: Drivers of Genome Evolution. Science 303: 1626-1632.
    • (2004) Science , vol.303 , pp. 1626-1632
    • Kazazian, H.H.1
  • 6
    • 0036021699 scopus 로고    scopus 로고
    • Transposable elements and the evolution of genome size in eukaryotes
    • Kidwell MG, (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115: 49-63.
    • (2002) Genetica , vol.115 , pp. 49-63
    • Kidwell, M.G.1
  • 7
    • 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, et al. (2006) Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Research 16: 1262-1269.
    • (2006) Genome Research , vol.16 , pp. 1262-1269
    • Piegu, B.1    Guyot, R.2    Picault, N.3    Roulin, A.4    Saniyal, A.5
  • 8
    • 70450202132 scopus 로고    scopus 로고
    • The B73 Maize Genome: Complexity, Diversity, and Dynamics
    • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326: 1112-1115.
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3    Stein, J.C.4    Wei, F.5
  • 9
    • 84858140069 scopus 로고    scopus 로고
    • Methylation Dynamics in the Early Mammalian Embryo: Implications of Genome Reprogramming Defects for Development
    • DNA Methylation: Development, Genetic Disease and Cancer: Springer Berlin Heidelberg
    • Doerfler W, Böhm P, Haaf T, (2006) Methylation Dynamics in the Early Mammalian Embryo: Implications of Genome Reprogramming Defects for Development. pp. 13-22 DNA Methylation: Development, Genetic Disease and Cancer: Springer Berlin Heidelberg.
    • (2006) , pp. 13-22
    • Doerfler, W.1    Böhm, P.2    Haaf, T.3
  • 10
    • 33845880624 scopus 로고    scopus 로고
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S, (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet 39: 61-69.
    • (2007) Nature Genet , vol.39 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5
  • 11
    • 0042027896 scopus 로고    scopus 로고
    • Structural Dynamics of Eukaryotic Chromosome Evolution
    • Eichler EE, Sankoff D, (2003) Structural Dynamics of Eukaryotic Chromosome Evolution. Science 301: 793-797.
    • (2003) Science , vol.301 , pp. 793-797
    • Eichler, E.E.1    Sankoff, D.2
  • 12
    • 33846978695 scopus 로고    scopus 로고
    • Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
    • Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes. Science 315: 848-853.
    • (2007) Science , vol.315 , pp. 848-853
    • Stranger, B.E.1    Forrest, M.S.2    Dunning, M.3    Ingle, C.E.4    Beazley, C.5
  • 14
    • 77954719711 scopus 로고    scopus 로고
    • The evolutionary ecology of clonally propagated domesticated plants
    • McKey D, Elias M, Pujol B, Duputié A, (2009) The evolutionary ecology of clonally propagated domesticated plants. New Phytologist 186: 318-332.
    • (2009) New Phytologist , vol.186 , pp. 318-332
    • McKey, D.1    Elias, M.2    Pujol, B.3    Duputié, A.4
  • 15
    • 0034914782 scopus 로고    scopus 로고
    • Somatic Mutations in Organisms with Complex Life Histories
    • Orive ME, (2001) Somatic Mutations in Organisms with Complex Life Histories. Theoretical Population Biology 59: 235-249.
    • (2001) Theoretical Population Biology , vol.59 , pp. 235-249
    • Orive, M.E.1
  • 18
    • 34247379370 scopus 로고    scopus 로고
    • Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers
    • Moncada X, Pelsy F, Merdinoglu D, Hinrichsen P, (2006) Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers. Genome 49: 1459-1472.
    • (2006) Genome , vol.49 , pp. 1459-1472
    • Moncada, X.1    Pelsy, F.2    Merdinoglu, D.3    Hinrichsen, P.4
  • 19
    • 4143126896 scopus 로고    scopus 로고
    • Diversification within grapevine cultivars goes through chimeric states
    • Hocquigny S, Pelsy F, Dumas V, Kindt S, Heloir MC, et al. (2004) Diversification within grapevine cultivars goes through chimeric states. Genome 47: 579-589.
    • (2004) Genome , vol.47 , pp. 579-589
    • Hocquigny, S.1    Pelsy, F.2    Dumas, V.3    Kindt, S.4    Heloir, M.C.5
  • 20
    • 0036936126 scopus 로고    scopus 로고
    • Molecular tools for clone identification: the case of the grapevine cultivar Traminer
    • Imazio S, Labra M, Grassi F, Winfield M, Bardini M, et al. (2002) Molecular tools for clone identification: the case of the grapevine cultivar "Traminer". Plant Breeding 121: 531-535.
    • (2002) Plant Breeding , vol.121 , pp. 531-535
    • Imazio, S.1    Labra, M.2    Grassi, F.3    Winfield, M.4    Bardini, M.5
  • 21
    • 77950022454 scopus 로고    scopus 로고
    • An extensive study of the genetic diversity within seven French wine grape variety collections
    • Pelsy F, Hocquigny S, Moncada X, Barbeau G, Forget D, et al. (2010) An extensive study of the genetic diversity within seven French wine grape variety collections. TAG Theoretical and Applied Genetics 120: 1219-1231.
    • (2010) TAG Theoretical and Applied Genetics , vol.120 , pp. 1219-1231
    • Pelsy, F.1    Hocquigny, S.2    Moncada, X.3    Barbeau, G.4    Forget, D.5
  • 22
    • 62949169906 scopus 로고    scopus 로고
    • Clonal Variation in Pinot noir Revealed by S-SAP Involving Universal Retrotransposon-Based Sequences
    • Wegscheider E, Benjak A, Forneck A, (2009) Clonal Variation in Pinot noir Revealed by S-SAP Involving Universal Retrotransposon-Based Sequences. Am J Enol Vitic 60: 104-109.
    • (2009) Am J Enol Vitic , vol.60 , pp. 104-109
    • Wegscheider, E.1    Benjak, A.2    Forneck, A.3
  • 23
    • 0034030770 scopus 로고    scopus 로고
    • Cloning and characterization of Vine-1, a LTR- retrotransposon-like element in Vitis vinifera L and other Vitis species
    • Verries C, Bes C, This P, Tesniere C, (2000) Cloning and characterization of Vine-1, a LTR- retrotransposon-like element in Vitis vinifera L and other Vitis species. Genome 43: 366-376.
    • (2000) Genome , vol.43 , pp. 366-376
    • Verries, C.1    Bes, C.2    This, P.3    Tesniere, C.4
  • 24
    • 2342541085 scopus 로고    scopus 로고
    • Vine-1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping
    • Labra M, Imazio S, Grassi F, Rossoni M, Sala F, (2004) Vine-1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping. Plant Breeding 123: 180-185.
    • (2004) Plant Breeding , vol.123 , pp. 180-185
    • Labra, M.1    Imazio, S.2    Grassi, F.3    Rossoni, M.4    Sala, F.5
  • 25
    • 33747209106 scopus 로고    scopus 로고
    • Historical origins and genetic diversity of wine grapes
    • This P, Lacombe T, Thomas MR, (2006) Historical origins and genetic diversity of wine grapes. Trends in Genetics 22: 511-519.
    • (2006) Trends in Genetics , vol.22 , pp. 511-519
    • This, P.1    Lacombe, T.2    Thomas, M.R.3
  • 27
    • 34848886909 scopus 로고    scopus 로고
    • The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    • Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
    • (2007) Nature , vol.449 , pp. 463-467
    • Jaillon, O.1    Aury, J.M.2    Noel, B.3    Policriti, A.4    Clepet, C.5
  • 28
    • 41249098849 scopus 로고    scopus 로고
    • A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety
    • Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, et al. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLoS ONE 2: e1326.
    • (2007) PLoS ONE , vol.2
    • Velasco, R.1    Zharkikh, A.2    Troggio, M.3    Cartwright, D.A.4    Cestaro, A.5
  • 29
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics 24: 133-141.
    • (2008) Trends in Genetics , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 30
    • 57649121742 scopus 로고    scopus 로고
    • Next-generation genetics in plants
    • Nordborg M, Weigel D, (2008) Next-generation genetics in plants. Nature 456: 720-723.
    • (2008) Nature , vol.456 , pp. 720-723
    • Nordborg, M.1    Weigel, D.2
  • 31
    • 0031978181 scopus 로고    scopus 로고
    • Base-Calling of Automated Sequencer Traces UsingPhred II. Error Probabilities
    • Ewing B, Green P, (1998) Base-Calling of Automated Sequencer Traces UsingPhred II. Error Probabilities. Genome Research 8: 186-194.
    • (1998) Genome Research , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 32
    • 0034284437 scopus 로고    scopus 로고
    • Repbase Update: a database and an electronic journal of repetitive elements
    • Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2000) Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet 9: 418-420.
    • (2000) Trends Genet , vol.9 , pp. 418-420
    • Jurka, J.1    Kapitonov, V.V.2    Pavlicek, A.3    Klonowski, P.4    Kohany, O.5
  • 34
    • 0030991387 scopus 로고    scopus 로고
    • Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP)
    • Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, et al. (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Molecular and General Genetics MGG 253: 687-694.
    • (1997) Molecular and General Genetics MGG , vol.253 , pp. 687-694
    • Waugh, R.1    McLean, K.2    Flavell, A.J.3    Pearce, S.R.4    Kumar, A.5
  • 35
    • 0005814023 scopus 로고
    • Mathematical model for studying genetic variation in terms of restriction endonucleases
    • Nei M, Li WH, (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences 76: 5269-5273.
    • (1979) Proceedings of the National Academy of Sciences , vol.76 , pp. 5269-5273
    • Nei, M.1    Li, W.H.2
  • 36
    • 36249023071 scopus 로고    scopus 로고
    • A unified classification system for eukaryotic transposable elements
    • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982.
    • (2007) Nat Rev Genet , vol.8 , pp. 973-982
    • Wicker, T.1    Sabot, F.2    Hua-Van, A.3    Bennetzen, J.L.4    Capy, P.5
  • 39
    • 79955028255 scopus 로고    scopus 로고
    • Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data
    • Sabot F, Picault N, El-Baidouri M, Llauro C, Chaparro C, et al. (2011) Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. The Plant Journal 66: 241-246.
    • (2011) The Plant Journal , vol.66 , pp. 241-246
    • Sabot, F.1    Picault, N.2    El-Baidouri, M.3    Llauro, C.4    Chaparro, C.5
  • 40
    • 77953006646 scopus 로고    scopus 로고
    • The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
    • Atanur SS, Birol Än, Guryev V, Hirst M, Hummel O, et al. (2010) The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Research 20: 791-803.
    • (2010) Genome Research , vol.20 , pp. 791-803
    • Atanur, S.S.1    Birol, A.2    Guryev, V.3    Hirst, M.4    Hummel, O.5
  • 41
    • 43649086914 scopus 로고    scopus 로고
    • Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp sativa
    • Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, et al. (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp sativa. Bmc Plant Biology 8.
    • (2008) Bmc Plant Biology , vol.8
    • Le Cunff, L.1    Fournier-Level, A.2    Laucou, V.3    Vezzulli, S.4    Lacombe, T.5
  • 43
    • 0036250001 scopus 로고    scopus 로고
    • Plant transposable elements: where genetics meets genomics
    • Feschotte C, Jiang N, Wessler SR, (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3: 329-341.
    • (2002) Nat Rev Genet , vol.3 , pp. 329-341
    • Feschotte, C.1    Jiang, N.2    Wessler, S.R.3
  • 45
    • 55249105198 scopus 로고    scopus 로고
    • Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome
    • Moisy C, Garrison K, Meredith C, Pelsy F, (2008) Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome. BMC Genomics 9: 469.
    • (2008) BMC Genomics , vol.9 , pp. 469
    • Moisy, C.1    Garrison, K.2    Meredith, C.3    Pelsy, F.4
  • 46
  • 47
    • 77950094520 scopus 로고    scopus 로고
    • Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)
    • Fournier-Level A, Lacombe T, Le Cunff L, Boursiquot JM, This P, (2010) Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.). Heredity 104: 351-362.
    • (2010) Heredity , vol.104 , pp. 351-362
    • Fournier-Level, A.1    Lacombe, T.2    Le Cunff, L.3    Boursiquot, J.M.4    This, P.5
  • 48
    • 78650992156 scopus 로고    scopus 로고
    • An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods
    • Carrier G, Santoni S, Rodier-Goud M, Canaguier A, Kochko Ad, et al. (2011) An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. American Journal of Botany 98: e13-e15.
    • (2011) American Journal of Botany , vol.98
    • Carrier, G.1    Santoni, S.2    Rodier-Goud, M.3    Canaguier, A.4    Kochko, A.5
  • 49
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 51
    • 50649122770 scopus 로고    scopus 로고
    • EagleView: A genome assembly viewer for next-generation sequencing technologies
    • Huang W, Marth G, (2008) EagleView: A genome assembly viewer for next-generation sequencing technologies. Genome Research 18: 1538-1543.
    • (2008) Genome Research , vol.18 , pp. 1538-1543
    • Huang, W.1    Marth, G.2
  • 52
    • 84858120718 scopus 로고    scopus 로고
    • Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
    • Chen N, (2002) Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences.
    • (2002)
    • Chen, N.1
  • 53
    • 69449083571 scopus 로고    scopus 로고
    • High-throughput retrotransposon-based fluorescent markers: improved information content and allele discrimination
    • Knox M, Moreau C, Lipscombe J, Baker D, Ellis N, (2009) High-throughput retrotransposon-based fluorescent markers: improved information content and allele discrimination. Plant Methods.
    • (2009) Plant Methods
    • Knox, M.1    Moreau, C.2    Lipscombe, J.3    Baker, D.4    Ellis, N.5
  • 55
    • 44849114374 scopus 로고    scopus 로고
    • Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm
    • DeBarry J, Liu R, Bennetzen J, (2008) Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 9: 235.
    • (2008) BMC Bioinformatics , vol.9 , pp. 235
    • DeBarry, J.1    Liu, R.2    Bennetzen, J.3
  • 56
    • 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 JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 57
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2


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