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Volumn 287, Issue 1, 2010, Pages 19-28

Structure and evolution of full-length LTR retrotransposons in rice genome

Author keywords

Element structure; Insertion time; LTR retrotransposons; LTR FINDER; Rice genome

Indexed keywords

JAPONICA; MYA; ORYZA SATIVA;

EID: 77952950482     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-010-0285-2     Document Type: Article
Times cited : (11)

References (51)
  • 1
    • 59949097135 scopus 로고    scopus 로고
    • Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome
    • Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL (2009) Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res 19: 243-254.
    • (2009) Genome Res , vol.19 , pp. 243-254
    • Baucom, R.S.1    Estill, J.C.2    Leebens-Mack, J.3    Bennetzen, J.L.4
  • 2
    • 40449139336 scopus 로고    scopus 로고
    • Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
    • Belancio VP, Hedges DJ, Deininger P (2008) Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 18: 343-358.
    • (2008) Genome Res , vol.18 , pp. 343-358
    • Belancio, V.P.1    Hedges, D.J.2    Deininger, P.3
  • 3
    • 23844460513 scopus 로고    scopus 로고
    • What transposable elements tell us about genome organization and evolution: The case of Drosophila
    • Biemont C, Vieira C (2005) What transposable elements tell us about genome organization and evolution: the case of Drosophila. Cytogenet Genome Res 110: 25-34.
    • (2005) Cytogenet Genome Res , vol.110 , pp. 25-34
    • Biemont, C.1    Vieira, C.2
  • 4
    • 0035997904 scopus 로고    scopus 로고
    • Transposable elements and the evolution of eukaryotic complexity
    • Bowen NJ, Jordan IK (2002) Transposable elements and the evolution of eukaryotic complexity. Curr Issues Mol Biol 4: 65-76.
    • (2002) Curr Issues Mol Biol , vol.4 , pp. 65-76
    • Bowen, N.J.1    Jordan, I.K.2
  • 5
    • 0037633476 scopus 로고    scopus 로고
    • Plant LTR-retrotransposons and MITEs: Control of transposition and impact on the evolution of plant genes and genomes
    • Casacuberta JM, Santiago N (2003) Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311: 1-11.
    • (2003) Gene , vol.311 , pp. 1-11
    • Casacuberta, J.M.1    Santiago, N.2
  • 7
    • 0031908204 scopus 로고    scopus 로고
    • Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice
    • Chen M, SanMiguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435-443.
    • (1998) Genetics , vol.148 , pp. 435-443
    • Chen, M.1    Sanmiguel, P.2    Bennetzen, J.L.3
  • 8
    • 0035211340 scopus 로고    scopus 로고
    • Toward a cytological characterization of the rice genome
    • Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001) Toward a cytological characterization of the rice genome. Genome Res 11: 2133-2141.
    • (2001) Genome Res , vol.11 , pp. 2133-2141
    • Cheng, Z.1    Buell, C.R.2    Wing, R.A.3    Gu, M.4    Jiang, J.5
  • 10
    • 0036061848 scopus 로고    scopus 로고
    • Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis
    • Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079.
    • (2002) Genome Res , vol.12 , pp. 1075-1079
    • Devos, K.M.1    Brown, J.K.2    Bennetzen, J.L.3
  • 11
    • 31144442173 scopus 로고    scopus 로고
    • Horizontal transfer of a plant transposon
    • Diao X, Freeling M, Lisch D (2006) Horizontal transfer of a plant transposon. PLoS Biol 4: e5.
    • (2006) PLoS Biol , vol.4
    • Diao, X.1    Freeling, M.2    Lisch, D.3
  • 12
    • 33645526445 scopus 로고    scopus 로고
    • Retrotransposon sequence variation in four asexual plant species
    • Docking TR, Saade FE, Elliott MC, Schoen DJ (2006) Retrotransposon sequence variation in four asexual plant species. J Mol Evol 62: 375-387.
    • (2006) J Mol Evol , vol.62 , pp. 375-387
    • Docking, T.R.1    Saade, F.E.2    Elliott, M.C.3    Schoen, D.J.4
  • 13
    • 0024505998 scopus 로고
    • Eukaryotic transposable elements and genome evolution
    • Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5: 103-107.
    • (1989) Trends Genet , vol.5 , pp. 103-107
    • Finnegan, D.J.1
  • 14
    • 2442657861 scopus 로고    scopus 로고
    • Evolutionary history of Oryza sativa LTR retrotransposons: A preliminary survey of the rice genome sequences
    • Gao L, McCarthy EM, Ganko EW, McDonald JF (2004) Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genom 5: 18.
    • (2004) BMC Genom , vol.5 , pp. 18
    • Gao, L.1    McCarthy, E.M.2    Ganko, E.W.3    McDonald, J.F.4
  • 15
    • 0029812835 scopus 로고    scopus 로고
    • Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
    • Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93: 10274-10279.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 10274-10279
    • Gaut, B.S.1    Morton, B.R.2    McCaig, B.C.3    Clegg, M.T.4
  • 17
    • 0034103860 scopus 로고    scopus 로고
    • Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation
    • Hirochika H, Okamoto H, Kakutani T (2000) Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12: 357-369.
    • (2000) Plant Cell , vol.12 , pp. 357-369
    • Hirochika, H.1    Okamoto, H.2    Kakutani, T.3
  • 20
    • 0034612315 scopus 로고    scopus 로고
    • Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence
    • Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Pro Natl Acad Sci USA 97: 6603-6607.
    • (2000) Pro Natl Acad Sci USA , vol.97 , pp. 6603-6607
    • Kalendar, R.1    Tanskanen, J.2    Immonen, S.3    Nevo, E.4    Schulman, A.H.5
  • 21
    • 37249012285 scopus 로고    scopus 로고
    • Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes
    • Kashkush K, Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177: 1975-1985.
    • (2007) Genetics , vol.177 , pp. 1975-1985
    • Kashkush, K.1    Khasdan, V.2
  • 22
    • 0034160156 scopus 로고    scopus 로고
    • Transposable elements and host genome evolution
    • Kidwell MG, Lisch DR (2000) Transposable elements and host genome evolution. Trends Ecol Evol 15: 95-99.
    • (2000) Trends Ecol Evol , vol.15 , pp. 95-99
    • Kidwell, M.G.1    Lisch, D.R.2
  • 23
    • 0043030233 scopus 로고    scopus 로고
    • Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma
    • Komatsu M, Shimamoto K, Kyozuka J (2003) Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma. Plant Cell 15: 1934-1944.
    • (2003) Plant Cell , vol.15 , pp. 1934-1944
    • Komatsu, M.1    Shimamoto, K.2    Kyozuka, J.3
  • 25
    • 0033645667 scopus 로고    scopus 로고
    • Retrotransposon activation followed by rapid repression in introgressed rice plants
    • Liu B, Wendel JF (2000) Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome 43: 874-880.
    • (2000) Genome , vol.43 , pp. 874-880
    • Liu, B.1    Wendel, J.F.2
  • 26
    • 4344616881 scopus 로고    scopus 로고
    • Rapid recent growth and divergence of rice nuclear genomes
    • Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101: 12404-12410.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 12404-12410
    • Ma, J.1    Bennetzen, J.L.2
  • 27
    • 31044442399 scopus 로고    scopus 로고
    • Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice
    • Ma J, Bennetzen JL (2006) Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci USA 103: 383-388.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 383-388
    • Ma, J.1    Bennetzen, J.L.2
  • 28
    • 2342466982 scopus 로고    scopus 로고
    • Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
    • Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860-869.
    • (2004) Genome Res , vol.14 , pp. 860-869
    • Ma, J.1    Devos, K.M.2    Bennetzen, J.L.3
  • 29
    • 47149097145 scopus 로고    scopus 로고
    • LTR retrotransposons and the evolution of dosage compensation in Drosophila
    • Matyunina LV, Bowen NJ, McDonald JF (2008) LTR retrotransposons and the evolution of dosage compensation in Drosophila. BMC Mol Biol 9: 55.
    • (2008) BMC Mol Biol , vol.9 , pp. 55
    • Matyunina, L.V.1    Bowen, N.J.2    McDonald, J.F.3
  • 31
    • 0034755894 scopus 로고    scopus 로고
    • Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome
    • Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11: 1660-1676.
    • (2001) Genome Res , vol.11 , pp. 1660-1676
    • Meyers, B.C.1    Tingey, S.V.2    Morgante, M.3
  • 32
    • 16344393155 scopus 로고    scopus 로고
    • Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice
    • Nagaki K, Neumann P, Zhang D, Ouyang S, Buell CR, Cheng Z, Jiang J (2005) Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice. Mol Biol Evol 22: 845-855.
    • (2005) Mol Biol Evol , vol.22 , pp. 845-855
    • Nagaki, K.1    Neumann, P.2    Zhang, D.3    Ouyang, S.4    Buell, C.R.5    Cheng, Z.6    Jiang, J.7
  • 33
    • 0035212395 scopus 로고    scopus 로고
    • Silencing of transposable elements in plants
    • Okamoto H, Hirochika H (2001) Silencing of transposable elements in plants. Trends Plant Sci 6: 527-534.
    • (2001) Trends Plant Sci , vol.6 , pp. 527-534
    • Okamoto, H.1    Hirochika, H.2
  • 34
    • 0035058360 scopus 로고    scopus 로고
    • Evolution of genome size: New approaches to an old problem
    • Petrov DA (2001) Evolution of genome size: new approaches to an old problem. Trends Genet 17: 23-28.
    • (2001) Trends Genet , vol.17 , pp. 23-28
    • Petrov, D.A.1
  • 35
    • 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 et al (2006) Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16: 1262-1269.
    • (2006) Genome Res , vol.16 , pp. 1262-1269
    • Piegu, B.1    Guyot, R.2    Picault, N.3
  • 37
    • 33745873501 scopus 로고    scopus 로고
    • Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome
    • Soleimani VD, Baum BR, Johnson DA (2006) Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome. Genome 49: 389-396.
    • (2006) Genome , vol.49 , pp. 389-396
    • Soleimani, V.D.1    Baum, B.R.2    Johnson, D.A.3
  • 39
    • 33845186134 scopus 로고    scopus 로고
    • Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution
    • Vitte C, Bennetzen JL (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103: 17638-17643.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17638-17643
    • Vitte, C.1    Bennetzen, J.L.2
  • 40
    • 0037387430 scopus 로고    scopus 로고
    • Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L
    • Vitte C, Panaud O (2003) Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol 20: 528-540.
    • (2003) Mol Biol Evol , vol.20 , pp. 528-540
    • Vitte, C.1    Panaud, O.2
  • 41
    • 23844543047 scopus 로고    scopus 로고
    • LTR retrotransposons and flowering plant genome size: Emergence of the increase/decrease model
    • Vitte C, Panaud O (2005) LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 110: 91-107.
    • (2005) Cytogenet Genome Res , vol.110 , pp. 91-107
    • Vitte, C.1    Panaud, O.2
  • 42
    • 34547740136 scopus 로고    scopus 로고
    • LTR retrotransposons in rice (Oryza sativa, L.): Recent burst amplifications followed by rapid DNA loss
    • Vitte C, Panaud O, Quesneville H (2007) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genom 8: 218.
    • (2007) BMC Genom , vol.8 , pp. 218
    • Vitte, C.1    Panaud, O.2    Quesneville, H.3
  • 43
    • 51349167797 scopus 로고    scopus 로고
    • LTR retrotransposon landscape in Medicago truncatula: More rapid removal than in rice
    • Wang H, Liu JS (2008) LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genom 9: 382.
    • (2008) BMC Genom , vol.9 , pp. 382
    • Wang, H.1    Liu, J.S.2
  • 44
    • 57749085447 scopus 로고    scopus 로고
    • Replication of nonautonomous retroelements in soybean appears to be both recent and common
    • Wawrzynski A, Ashfield T, Chen NW et al (2008) Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiol 148: 1760-1771.
    • (2008) Plant Physiol , vol.148 , pp. 1760-1771
    • Wawrzynski, A.1    Ashfield, T.2    Chen, N.W.3
  • 45
    • 0034612263 scopus 로고    scopus 로고
    • Retrotransposon-mediated genome evolution on a local ecological scale
    • Wendel JF, Wessler SR (2000) Retrotransposon-mediated genome evolution on a local ecological scale. Proc Natl Acad Sci USA 97: 6250-6252.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 6250-6252
    • Wendel, J.F.1    Wessler, S.R.2
  • 46
    • 0030207150 scopus 로고    scopus 로고
    • Turned on by stress. Plant retrotransposons
    • Wessler SR (1996) Turned on by stress. Plant retrotransposons. Curr Biol 6: 959-961.
    • (1996) Curr Biol , vol.6 , pp. 959-961
    • Wessler, S.R.1
  • 47
    • 33845223393 scopus 로고    scopus 로고
    • Transposable elements and the evolution of eukaryotic genomes
    • Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci USA 103: 17600-17601.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 17600-17601
    • Wessler, S.R.1
  • 48
    • 34347381116 scopus 로고    scopus 로고
    • Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families
    • Wicker T, Keller B (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res 17: 1072-1081.
    • (2007) Genome Res , vol.17 , pp. 1072-1081
    • Wicker, T.1    Keller, B.2
  • 50
    • 58449090877 scopus 로고    scopus 로고
    • Diverged copies of the seed regulatory Opaque-2 gene by a segmental duplication in the progenitor genome of rice, sorghum, and maize
    • Xu JH, Messing J (2008) Diverged copies of the seed regulatory Opaque-2 gene by a segmental duplication in the progenitor genome of rice, sorghum, and maize. Mol Plant 1: 760-769.
    • (2008) Mol Plant , vol.1 , pp. 760-769
    • Xu, J.H.1    Messing, J.2
  • 51
    • 34547592867 scopus 로고    scopus 로고
    • LTR-FINDER: An efficient tool for the prediction of full-length LTR retrotransposons
    • Xu Z, Wang H (2007) LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35: W265-W268.
    • (2007) Nucleic Acids Res , vol.35
    • Xu, Z.1    Wang, H.2


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