1932

Abstract

Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in . Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants.

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2014-04-29
2024-06-20
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Literature Cited

  1. Barbaglia AM, Klusman KM, Higgins J, Shaw JR, Hannah LC, Lal SK. 1.  2012. Gene capture by Helitron transposons reshuffles the transcriptome of maize. Genetics 190:965–75 [Google Scholar]
  2. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P. 2.  et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–12 [Google Scholar]
  3. Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A. 3.  et al. 2009. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet. 5:e1000732 [Google Scholar]
  4. Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. 4.  2009. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19:243–54 [Google Scholar]
  5. Bennett MD. 5.  1972. Nuclear DNA content and minimum generation time in herbaceous plants. Proc. R. Soc. B 181:109–35 [Google Scholar]
  6. Bennetzen JL. 6.  2000. The many hues of plant heterochromatin. Genome Biol. 1:reviews107 [Google Scholar]
  7. Bennetzen JL. 7.  2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42:251–69 [Google Scholar]
  8. Bennetzen JL. 8.  2007. Patterns in grass genome evolution. Curr. Opin. Plant Biol. 10:176–81 [Google Scholar]
  9. Bennetzen JL, Coleman C, Liu RY, Ma JX, Ramakrishna W. 9.  2004. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7:732–36 [Google Scholar]
  10. Bennetzen JL, Kellogg EA. 10.  1997. Do plants have a one-way ticket to genomic obesity?. Plant Cell 9:1509–14 [Google Scholar]
  11. Bennetzen JL, Ma JX, Devos K. 11.  2005. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95:127–32 [Google Scholar]
  12. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J. 12.  et al. 2012. Reference genome sequence of the model plant Setaria. Nat. Biotechnol. 30:555–61 [Google Scholar]
  13. Bhaya D, Davison M, Barrangou R. 13.  2011. CRISPR-Cas systems in Bacteria and Archaea: versatile small RNAs for adaptive defense and regulation. Annu. Rev. Genet. 45:273–97 [Google Scholar]
  14. Bundock P, Hooykaas P. 14.  2005. An Arabidopsis hAT-like transposase is essential for plant development. Nature 436:282–84 [Google Scholar]
  15. Casacuberta E, González J. 15.  2013. The impact of transposable elements in environmental adaptation. Mol. Ecol. 22:1503–17 [Google Scholar]
  16. Casadesús J, Low D. 16.  2006. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70:830–56 [Google Scholar]
  17. Charlesworth D, Charlesworth B. 17.  1995. Transposable elements in inbreeding and outbreeding populations. Genetics 140:415–17 [Google Scholar]
  18. Chen JC, Greenblatt IM, Dellaporta SL. 18.  1987. Transposition of Ac from the P locus of maize into unreplicated chromosomal sites. Genetics 117:109–16 [Google Scholar]
  19. Chen JF, Huang QF, Gao DY, Wang JY, Lang YS. 19.  et al. 2013. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat. Commun. 4:1595 [Google Scholar]
  20. Cheng C, Daigen M, Hirochika H. 20.  2006. Epigenetic regulation of the rice retrotransposon Tos17. Mol. Genet. Genomics 276:378–90 [Google Scholar]
  21. Chia JM, Song C, Bradbury PJ, Costich D, de Leon N. 21.  et al. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44:803–7 [Google Scholar]
  22. Clark JB, Kidwell MG. 22.  1997. A phylogenetic perspective on P transposable element evolution in Drosophila. Proc. Natl. Acad. Sci. USA 94:11428–33 [Google Scholar]
  23. Cubas P, Vincent C, Coen E. 23.  1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401:157–61 [Google Scholar]
  24. Cui X, Jin P, Cui X, Gu L, Lu Z. 24.  et al. 2013. Control of transposon activity by a histone H3K4 demethylase in rice. Proc. Natl. Acad. Sci. USA 110:1953–58 [Google Scholar]
  25. Dawe RK, Henikoff S. 25.  2006. Centromeres put epigenetics in the driver's seat. Trends Biochem. Sci. 31:662–69 [Google Scholar]
  26. de Meaux J, Pecinka A. 26.  2012. The Arabidopsis genus: an emerging model to elucidate the molecular basis of interspecific differences in transposable element activity. Mob. Genet. Elem. 2:142–44 [Google Scholar]
  27. de Souza FSJ, Franchini LF, Rubinstein M. 27.  2013. Exaptation of transposable elements into novel cis-regulatory elements: Is the evidence always strong?. Mol. Biol. Evol. 30:1239–51 [Google Scholar]
  28. Devos KM, Brown JKM, Bennetzen JL. 28.  2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12:1075–79 [Google Scholar]
  29. Díez CM, Gaut BS, Meca E, Scheinvar E, Montes-Hernandez S. 29.  et al. 2013. Genome size variation in wild and cultivated maize along altitudinal gradients. New Phytol. 199:264–76 [Google Scholar]
  30. Doolittle WF, Sapienza C. 30.  1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601–3 [Google Scholar]
  31. Du CG, Hoffman A, He LM, Caronna J, Dooner HK. 31.  2011. The complete Ac/Ds transposon family of maize. BMC Genomics 12:588 [Google Scholar]
  32. El Baidouri M, Panaud O. 32.  2013. Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biol. Evol. 5:954–65 [Google Scholar]
  33. Elrouby N, Bureau TE. 33.  2010. Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize. Plant Physiol. 153:1413–24 [Google Scholar]
  34. Engels WR. 34.  1997. Invasions of P elements. Genetics 145:11–15 [Google Scholar]
  35. Estep MC, DeBarry JD, Bennetzen JL. 35.  2013. The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity 110:194–204 [Google Scholar]
  36. Fedoroff NV. 36.  2013. Plant Transposons and Genome Dynamics in Evolution Ames, IA: Wiley and Sons [Google Scholar]
  37. Fernandez L, Torregrosa L, Segura V, Bouquet A, Martinez-Zapater JM. 37.  2010. Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine. Plant J. 61:545–57 [Google Scholar]
  38. Feschotte C. 38.  2008. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9:397–405 [Google Scholar]
  39. Fortune PM, Roulin A, Panaud O. 39.  2008. Horizontal transfer of transposable elements in plants. Commun. Integr. Biol. 1:74–77 [Google Scholar]
  40. Fu HH, Zheng ZW, Dooner HK. 40.  2002. Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99:1082–87 [Google Scholar]
  41. Gao DY, Gill N, Kim HR, Walling JG, Zhang WL. 41.  et al. 2009. A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J. 60:820–31 [Google Scholar]
  42. Gao X, Hou Y, Ebina H, Levin HL, Voytas DF. 42.  2008. Chromodomains direct integration of retrotransposons to heterochromatin. Genome Res. 18:359–69 [Google Scholar]
  43. Gilbert W. 43.  1978. Why genes in pieces?. Nature 271:501 [Google Scholar]
  44. Goettel W, Messing J. 44.  2010. Divergence of gene regulation through chromosomal rearrangements. BMC Genomics 11:678 [Google Scholar]
  45. Gonzalez J, Petrov DA. 45.  2009. The adaptive role of transposable elements in the Drosophila genome. Gene 448:124–33 [Google Scholar]
  46. Grandbastien MA. 46.  1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3:181–87 [Google Scholar]
  47. Grandbastien MA, Spielmann A, Caboche M. 47.  1989. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant-cell genetics. Nature 337:376–80 [Google Scholar]
  48. Greilhuber J, Borsch T, Müller K, Worberg A, Porembski S, Barthlott W. 48.  2006. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol. 8:770–77 [Google Scholar]
  49. Hawkins JS, Proulx SR, Rapp RA, Wendel JF. 49.  2009. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc. Natl. Acad. Sci. USA 106:17811–16 [Google Scholar]
  50. Hayashi K, Yoshida H. 50.  2009. Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter. Plant J. 57:413–25 [Google Scholar]
  51. He F, Zhang X, Hu JY, Turck F, Dong X. 51.  et al. 2012. Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus. Mol. Biol. Evol. 29:1081–91 [Google Scholar]
  52. Hollister JD, Gaut BS. 52.  2009. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19:1419–28 [Google Scholar]
  53. Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS. 53.  2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl. Acad. Sci. USA 108:2322–27 [Google Scholar]
  54. Hudson ME, Lisch DR, Quail PH. 54.  2003. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J. 34:453–71 [Google Scholar]
  55. Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L. 55.  et al. 2013. Architecture and evolution of a minute plant genome. Nature 498:94–98 [Google Scholar]
  56. Ilic K, SanMiguel PJ, Bennetzen JL. 56.  2003. A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc. Natl. Acad. Sci. USA 100:12265–70 [Google Scholar]
  57. Ivics Z, Hackett PB, Plasterk RH, Izsvák Z. 57.  1997. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91:501–10 [Google Scholar]
  58. Jameson N, Georgelis N, Fouladbash E, Martens S, Hannah LC, Lal S. 58.  2008. Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize. Plant Mol. Biol. 67:295–304 [Google Scholar]
  59. Jiang N, Bao ZR, Zhang XY, Eddy SR, Wessler SR. 59.  2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569–73 [Google Scholar]
  60. Jiang N, Wessler SR. 60.  2001. Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements. Plant Cell 13:2553–64 [Google Scholar]
  61. Jin J, Ang XL, Ye X, Livingstone M, Harper JW. 61.  2008. Differential roles for checkpoint kinases in DNA damage-dependent degradation of the Cdc25A protein phosphatase. J. Biol. Chem. 283:19322–28 [Google Scholar]
  62. Jin YK, Bennetzen JL. 62.  1994. Integration and nonrandom mutation of a plasma-membrane proton ATPase gene fragment within the Bs1 retroelement of maize. Plant Cell 6:1177–86 [Google Scholar]
  63. Kajihara D, de Godoy F, Hamaji TA, Blanco SR, Van Sluys MA, Rossi M. 63.  2012. Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum. Genet Mol. Biol. 35:632–39 [Google Scholar]
  64. Kashkush K, Feldman M, Levy AA. 64.  2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160:1651–59 [Google Scholar]
  65. Kellogg EA, Bennetzen JL. 65.  2004. The evolution of nuclear genome structure in seed plants. Am. J. Bot. 91:1709–25 [Google Scholar]
  66. Kirchner J, Connolly CM, Sandmeyer SB. 66.  1995. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267:1488–91 [Google Scholar]
  67. Kirik A, Salomon S, Puchta H. 67.  2000. Species-specific double-strand break repair and genome evolution in plants. EMBO J. 19:5562–66 [Google Scholar]
  68. Konkel MK, Batzer MA. 68.  2010. A mobile threat to genome stability: the impact of non-LTR retrotransposons upon the human genome. Semin. Cancer Biol. 20:211–21 [Google Scholar]
  69. Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC. 69.  2003. The maize genome contains a Helitron insertion. Plant Cell 15:381–91 [Google Scholar]
  70. Langham RJ, Walsh J, Dunn M, Ko C, Goff SA, Freeling M. 70.  2004. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166:935–45 [Google Scholar]
  71. Lenoir A, Lavie L, Prieto JL, Goubely C, Cote JC. 71.  et al. 2001. The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana. Mol. Biol. Evol. 18:2315–22 [Google Scholar]
  72. Li JF, Norville JE, Aach J, McCormack M, Zhang DD. 72.  et al. 2013. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol. 31:688–91 [Google Scholar]
  73. Li Y, Dooner HK. 73.  2009. Excision of Helitron transposons in maize. Genetics 182:399–402 [Google Scholar]
  74. Li Y, Li CQ, Xia J, Jin YX. 74.  2011. Domestication of transposable elements into microRNA genes in plants. PLoS ONE 6:e19212 [Google Scholar]
  75. Lichten M, Haber JE. 75.  1989. Position effects in ectopic and allelic mitotic recombination in Saccharomyces cerevisiae. Genetics 123:261–68 [Google Scholar]
  76. Lin LF, Tang HB, Compton RO, Lemke C, Rainville LK. 76.  et al. 2011. Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage. Genomics 97:313–20 [Google Scholar]
  77. Lin RC, Ding L, Casola C, Ripoll DR, Feschotte C, Wang HY. 77.  2007. Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318:1302–5 [Google Scholar]
  78. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N. 78.  et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–76 [Google Scholar]
  79. Lisch D. 79.  2009. Epigenetic regulation of transposons in plants. Annu. Rev. Plant Biol 60:43–66 [Google Scholar]
  80. Lisch D, Bennetzen JL. 80.  2011. Transposable element origins of epigenetic gene regulation. Curr. Opin. Plant Biol. 14:156–61 [Google Scholar]
  81. Liu RY, Vitte C, Ma JX, Mahama AA, Dhliwayo T. 81.  et al. 2007. A GeneTrek analysis of the maize genome. Proc. Natl. Acad. Sci. USA 104:11844–49 [Google Scholar]
  82. Liu SZ, Yeh CT, Ji TM, Ying K, Wu HY. 82.  et al. 2009. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet. 5:e1000733 [Google Scholar]
  83. Lockton S, Gaut BS. 83.  2009. The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J. Mol. Evol. 68:80–89 [Google Scholar]
  84. Ma JX, Bennetzen JL. 84.  2004. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. USA 101:12404–10 [Google Scholar]
  85. Ma JX, Bennetzen JL. 85.  2006. Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc. Natl. Acad. Sci. USA 103:383–88 [Google Scholar]
  86. Ma JX, Wing RA, Bennetzen JL, Jackson SA. 86.  2007. Plant centromere organization: a dynamic structure with conserved functions. Trends Genet. 23:134–39 [Google Scholar]
  87. Madlung A, Tyagi AP, Watson B, Jiang HM, Kagochi T. 87.  et al. 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 41:221–30 [Google Scholar]
  88. McClintock B. 88.  1948. Mutable loci in maize. Carnegie Inst. Wash. Yearb. 47:155–69 [Google Scholar]
  89. McClintock B. 89.  1951. Chromosome organization and genic expression. Cold Spring Harb. Symp. 16:13–47 [Google Scholar]
  90. McClintock B. 90.  1956. Controlling elements and the gene. Cold Spring Harb. Symp. 21:197–216 [Google Scholar]
  91. McClintock B. 91.  1984. The significance of responses of the genome to challenge. Science 226:792–801 [Google Scholar]
  92. McCue AD, Nuthikattu S, Slotkin RK. 92.  2013. Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs. RNA Biol. 10:1379–95 [Google Scholar]
  93. McCue AD, Slotkin RK. 93.  2012. Transposable element small RNAs as regulators of gene expression. Trends Genet. 28:616–23 [Google Scholar]
  94. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A. 94.  2005. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37:997–1002 [Google Scholar]
  95. Mottinger JP, Johns MA, Freeling M. 95.  1984. Mutations of the Adh1 gene in maize following infection with barley stripe mosaic virus. Mol. Gen. Genet. 195:367–69 [Google Scholar]
  96. Nagy ED, Bennetzen JL. 96.  2008. Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster. Genome Res. 18:1918–23 [Google Scholar]
  97. Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN. 97.  et al. 2009. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461:1130–34 [Google Scholar]
  98. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC. 98.  et al. 2013. The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–84 [Google Scholar]
  99. Ogiwara I, Miya M, Ohshima K, Okada N. 99.  2002. V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res. 12:316–24 [Google Scholar]
  100. Okagaki RJ, Wessler SR. 100.  1988. Comparison of non-mutant and mutant waxy genes in rice and maize. Genetics 120:1137–43 [Google Scholar]
  101. Oliver KR, Greene WK. 101.  2009. Transposable elements: powerful facilitators of evolution. BioEssays 31:703–14 [Google Scholar]
  102. Orgel LE, Crick FHC. 102.  1980. Selfish DNA: the ultimate parasite. Nature 284:604–7 [Google Scholar]
  103. Panda K, Slotkin RK. 103.  2013. Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway. Plant Signal. Behav. 8:e25206 [Google Scholar]
  104. Pardue ML, DeBaryshe PG. 104.  2011. Retrotransposons that maintain chromosome ends. Proc. Natl. Acad. Sci. USA 108:20317–24 [Google Scholar]
  105. Pellicer J, Fay MF, Leitch IJ. 105.  2010. The largest eukaryotic genome of them all?. Bot. J. Linn. Soc. 164:10–15 [Google Scholar]
  106. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A. 106.  et al. 2006. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16:1262–69 [Google Scholar]
  107. Piriyapongsa J, Jordan IK. 107.  2008. Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814–21 [Google Scholar]
  108. Pritham EJ. 108.  2009. Transposable elements and factors influencing their success in eukaryotes. J. Hered. 100:648–55 [Google Scholar]
  109. Rebollo R, Romanish MT, Mager DL. 109.  2012. Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu. Rev. Genet. 46:21–42 [Google Scholar]
  110. Robbins TP, Walker EL, Kermicle JL, Alleman M, Dellaporta SL. 110.  1991. Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromosomal rearrangement. Genetics 129:271–83 [Google Scholar]
  111. Sabot F, Schulman AH. 111.  2006. Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity 97:381–88 [Google Scholar]
  112. SanMiguel P, Bennetzen JL. 112.  1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82:37–44 [Google Scholar]
  113. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 113.  1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20:43–45 [Google Scholar]
  114. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D. 114.  et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–68 [Google Scholar]
  115. Schaack S, Gilbert C, Feschotte C. 115.  2010. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol. Evol. 25:537–46 [Google Scholar]
  116. Scott L, LaFoe D, Weil CF. 116.  1996. Adjacent sequences influence DNA repair accompanying transposon excision in maize. Genetics 142:237–46 [Google Scholar]
  117. Sharma A, Wolfgruber TK, Presting GG. 117.  2013. Tandem repeats derived from centromeric retrotransposons. BMC Genomics 14:142 [Google Scholar]
  118. Simon SA, Meyers BC. 118.  2011. Small RNA-mediated epigenetic modifications in plants. Curr. Opin. Plant Biol. 14:148–55 [Google Scholar]
  119. Slotkin RK, Freeling M, Lisch D. 119.  2005. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat. Genet. 37:641–44 [Google Scholar]
  120. Slotkin RK, Martienssen R. 120.  2007. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8:272–85 [Google Scholar]
  121. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH. 121.  et al. 2009. Polyploidy and angiosperm diversification. Am. J. Bot. 96:336–48 [Google Scholar]
  122. Starling P, Saedler H. 122.  1972. Insertion mutations in microorganisms. Biochimie 54:177–85 [Google Scholar]
  123. Sun FL, Guo WW, Du JK, Ni ZF, Sun QX, Yao YY. 123.  2013. Widespread, abundant, and diverse TE-associated siRNAs in developing wheat grain. Gene 522:1–7 [Google Scholar]
  124. Tenaillon MI, Hollister JD, Gaut BS. 124.  2010. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15:471–78 [Google Scholar]
  125. Tikhonov AP, Bennetzen JL, Avramova ZV. 125.  2000. Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum. Plant Cell 12:249–64 [Google Scholar]
  126. Tsukahara S, Kawabe A, Kobayashi A, Ito T, Aizu T. 126.  et al. 2012. Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata. Genes Dev. 26:705–13 [Google Scholar]
  127. Vaissiere T, Sawan C, Herceg Z. 127.  2008. Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat. Res. 659:40–48 [Google Scholar]
  128. Vitte C, Bennetzen JL. 128.  2006. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc. Natl. Acad. Sci. USA 103:17638–43 [Google Scholar]
  129. Vitte C, Panaud O. 129.  2003. Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20:528–40 [Google Scholar]
  130. Wang QH, Dooner HK. 130.  2006. Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc. Natl. Acad. Sci. USA 103:17644–49 [Google Scholar]
  131. Wang W, Zheng HK, Fan CZ, Li J, Shi JJ. 131.  et al. 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18:1791–802 [Google Scholar]
  132. Weber B, Schmidt T. 132.  2009. Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain. Chromosome Res. 17:379–96 [Google Scholar]
  133. Wei LJ, Xiao ML, An ZS, Ma B, Mason AS. 133.  et al. 2013. New insights into nested long terminal repeat retrotransposons in Brassica species. Mol. Plant 6:470–82 [Google Scholar]
  134. White SE, Habera LF, Wessler SR. 134.  1994. Retrotransposons in the flanking regions of normal plant genes: a role for Copia-like elements in the evolution of gene structure and expression. Proc. Natl. Acad. Sci. USA 91:11792–96 [Google Scholar]
  135. Wicker T, Buchmann JP, Keller B. 135.  2010. Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res. 20:1229–37 [Google Scholar]
  136. Wicker T, Guyot R, Yahiaoui N, Keller B. 136.  2003. CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol. 132:52–63 [Google Scholar]
  137. Wicker T, Keller B. 137.  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. 17:1072–81 [Google Scholar]
  138. Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B. 138.  et al. 2011. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706–18 [Google Scholar]
  139. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P. 139.  et al. 2007. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8:973–82 [Google Scholar]
  140. Xiong Y, Eickbush TH. 140.  1990. Origin and evolution of retroelements based upon their reverse-transcriptase sequences. EMBO J. 9:3353–62 [Google Scholar]
  141. Yan YS, Zhang YM, Yang K, Sun ZX, Fu YP. 141.  et al. 2011. Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice. Plant J. 65:820–28 [Google Scholar]
  142. Yang LX, Bennetzen JL. 142.  2009. Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc. Natl. Acad. Sci. USA 106:19922–27 [Google Scholar]
  143. Yu SW, Li JJ, Luo LJ. 143.  2010. Complexity and specificity of precursor microRNAs driven by transposable elements in rice. Plant Mol. Biol. Rep. 28:502–11 [Google Scholar]
  144. Zedek F, Šmerda J, Šmarda P, Bureš P. 144.  2010. Correlated evolution of LTR retrotransposons and genome size in the genus Eleocharis. BMC Plant Biol. 10:265 [Google Scholar]
  145. Zeh DW, Zeh JA, Ishida Y. 145.  2009. Transposable elements and an epigenetic basis for punctuated equilibria. BioEssays 31:715–26 [Google Scholar]
  146. Zhang J, Peterson T. 146.  1999. Genome rearrangements by nonlinear transposons in maize. Genetics 153:1403–10 [Google Scholar]
  147. Ziolkowski PA, Koczyk G, Galganski L, Sadowski J. 147.  2009. Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Res. 37:3189–201 [Google Scholar]
  148. Zou S, Voytas DF. 148.  1997. Silent chromatin determines target preference of the Saccharomyces retrotransposon Ty5. Proc. Natl. Acad. Sci. USA 94:7412–16 [Google Scholar]
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