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Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).

Vonholdt BM, Takuno S, Gaut BS.

Mol Biol Evol. 2012 Oct;29(10):3193-203. Epub 2012 May 15.


Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian Z, Rizzon C, Du J, Zhu L, Bennetzen JL, Jackson SA, Gaut BS, Ma J.

Genome Res. 2009 Dec;19(12):2221-30. doi: 10.1101/gr.083899.108. Epub 2009 Sep 29.


Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison.

Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J.

Plant J. 2010 Aug;63(4):584-98. doi: 10.1111/j.1365-313X.2010.04263.x.


Retrotranspositions in orthologous regions of closely related grass species.

Du C, Swigonová Z, Messing J.

BMC Evol Biol. 2006 Aug 16;6:62.


LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice.

Wang H, Liu JS.

BMC Genomics. 2008 Aug 10;9:382. doi: 10.1186/1471-2164-9-382.


TEnest: automated chronological annotation and visualization of nested plant transposable elements.

Kronmiller BA, Wise RP.

Plant Physiol. 2008 Jan;146(1):45-59. Epub 2007 Nov 21.


Long terminal repeat retrotransposons of Oryza sativa.

McCarthy EM, Liu J, Lizhi G, McDonald JF.

Genome Biol. 2002 Sep 13;3(10):RESEARCH0053. Epub 2002 Sep 13.


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.

Genome Res. 2009 Feb;19(2):243-54. doi: 10.1101/gr.083360.108. Epub 2008 Nov 24.


TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato.

Yin H, Liu J, Xu Y, Liu X, Zhang S, Ma J, Du J.

PLoS One. 2013 Jul 4;8(7):e68587. doi: 10.1371/journal.pone.0068587. Print 2013.


Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice.

Ma J, Devos KM, Bennetzen JL.

Genome Res. 2004 May;14(5):860-9. Epub 2004 Apr 12.


Identification of an active LTR retrotransposon in rice.

Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D, Guiderdoni E, Panaud O.

Plant J. 2009 Jun;58(5):754-65. doi: 10.1111/j.1365-313X.2009.03813.x. Epub 2009 Feb 2. Erratum in: Plant J. 2009 Dec;60(5):929.


Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean.

Tian Z, Zhao M, She M, Du J, Cannon SB, Liu X, Xu X, Qi X, Li MW, Lam HM, Ma J.

Plant Cell. 2012 Nov;24(11):4422-36. doi: 10.1105/tpc.112.103630. Epub 2012 Nov 21.


Co-evolution of plant LTR-retrotransposons and their host genomes.

Zhao M, Ma J.

Protein Cell. 2013 Jul;4(7):493-501. doi: 10.1007/s13238-013-3037-6. Epub 2013 Jun 23. Review.


Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution.

El Baidouri M, Panaud O.

Genome Biol Evol. 2013;5(5):954-65. doi: 10.1093/gbe/evt025.

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