The contributions of transposable elements to the structure, function, and evolution of plant genomes

Annual Review of Plant Biology

Volumn 65, Issue , 2014, Pages 505-530

  Bennetzen, Jeffrey L ^a   Wang, Hao ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

Author keywords

epigenetics; gene regulation; genome rearrangement; genome size; transposon domestication

Indexed keywords

EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; PLANT; PLANT GENE; PLANT GENOME; REVIEW; TRANSPOSON;

BIOLOGICAL EVOLUTION; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; PLANTS;

EID: 84899743736     PISSN: 15435008     EISSN: 15452123     Source Type: Book Series    
DOI: 10.1146/annurev-arplant-050213-035811     Document Type: Review

References (148)

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