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Cited by 51Chromosomal and Genetic VariationsWheat and Barley Genetics and PathologyPlant Taxonomy and Phylogenetics

Methylation, transcription, and rearrangements of transposable elements in synthetic allopolyploids

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Yaakov, Beery, Kashkush, Khalil·2011·International Journal of Plant Genomics
DOI 10.1155/2011/569826PMC PMC3134107
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Abstract

Transposable elements (TEs) constitute over 90% of the wheat genome. It was suggested that "genomic stress" such as hybridity or polyploidy might activate transposons. Intensive investigations of various polyploid systems revealed that allopolyploidization event is associated with widespread changes in genome structure, methylation, and expression involving low- and high-copy, coding and noncoding sequences. Massive demethylation and transcriptional activation of TEs were also observed in newly formed allopolyploids. Massive proliferation, however, was reported for very limited number of TE families in various polyploidy systems. The aim of this review is to summarize the accumulated data on genetic and epigenetic dynamics of TEs, particularly in synthetic allotetraploid and allohexaploid wheat species. In addition, the underlying mechanisms and the potential biological significance of TE dynamics following allopolyploidization are discussed.

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  • Global DNA methylation is the most evaluated epigenetic somaclonal variation; in plants it is at higher levels than in other eukaryotes and is correlated with expression of different genes and changes in mobility of transposable elements.

    “The most evaluated epigenetic somaclonal variation is global DNA methylation, which, in plants, is at higher levels compared with other eukaryotes, and is correlated with the expression of different genes, and changes in the mobility of the numerous transposable elements presented in plant genomes [99,101,102,103,104,105,106,107,108,109].”

    From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as [105]

    The Introduction states that methylation of transposable elements is associated with their activation or silencing, and that transposable elements can affect nearby gene expression. It does not say that global DNA methylation is the most evaluated epigenetic somaclonal variation or that methylation levels in plants exceed those in other eukaryotes. Its comparison is between transposable elements and host genes within plants, not between plants and other eukaryotes. (LLM, conf=0.86)

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Research works printed but not linked: 62

  1. [1]Sabot F Guyot R Wicker T Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations Molecular Genetics and Genomics 2005 274 2 119 130 16034625
  2. [2]Wicker T Sabot F Hua-Van A A unified classification system for eukaryotic transposable elements Nature Reviews Genetics 2007 8 12 973 982 17984973
  3. [3]Slotkin RK Martienssen R Transposable elements and the epigenetic regulation of the genome Nature Reviews Genetics 2007 8 4 272 285 17363976
  4. [4]Feschotte C Pritham EJ DNA transposons and the evolution of eukaryotic genomes Annual Review of Genetics 2007 41 331 368 PMC2167627 18076328
  5. [5]Kashkush K Feldman M Levy AA Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat Nature Genetics 2003 33 1 102 106 12483211
  6. [6]Iida S Morita Y Choi JD Park KI Hoshino A Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories Advances in Biophysics 2004 38 141 159 15493332
  7. [7]Lockton S Gaut BS The contribution of transposable elements to expressed coding sequence in arabidopsis thaliana Journal of Molecular Evolution 2009 68 1 80 89 19125217
  8. [8]Gehring M Henikoff S DNA methylation and demethylation in arabidopsis The Arabidopsis Book 2008 American Society of Plant Biologists 1 14 PMC3243302 22303233
  9. [9]Cokus SJ Feng S Zhang X Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning Nature 2008 452 7184 215 219 18278030 PMC2377394
  10. [10]Kumar A Bennetzen JL Plant retrotransposons Annual Review of Genetics 1999 33 479 532 10690416
  11. [11]Rabinowicz PD Palmer LE May BP Genes and transposons are differentially methylated in plants, but not in mammals Genome Research 2003 13 12 2658 2664 14656970 PMC403807
  12. [12]Madlung A Comai L The effect of stress on genome regulation and structure Annals of Botany 2004 94 4 481 495 15319229 PMC4242226
  13. [13]Levy AA Feldman M The impact of polyploidy on grass genome evolution Plant Physiology 2002 130 4 1587 1593 12481041 PMC1540263
  14. [14]Ohno S Evolution by Gene Duplication 1970 New York, NY, USA Springer
  15. [15]Liu B Vega JM Feldman M Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences Genome 1998 41 4 535 542 9796102
  16. [16]Liu B Vega JM Segal G Abbo S Rodova M Feldman M Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences Genome 1998 41 2 272 277 9796102
  17. [17]Ozkan H Levy AA Feldman M Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group Plant Cell 2001 13 8 1735 1747 11487689 PMC139130
  18. [18]Shaked H Kashkush K Ozkan H Feldman M Levy AA Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat Plant Cell 2001 13 8 1749 1759 11487690 PMC139131
  19. [19]Han F Fedak G Guo W Liu B Rapid and repeatable elimination of a parental genome-specific repeat (pGc1R-1a) in newly synthesized wheat allopolyploids Genetics 2005 170 3 1239 1245 15911583 PMC1451191
  20. [20]Skalická K Lim KY Matyasek R Matzke M Leitch AR Kovarik A Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco New Phytologist 2005 166 1 291 303 15760371
  21. [21]Chen ZJ Pikaard CS Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance Genes and Development 1997 11 16 2124 2136 9284051 PMC316451
  22. [22]Chen ZJ Pikaard CS Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica Proceedings of the National Academy of Sciences of the United States of America 1997 94 7 3442 3447 9096413 PMC20389
  23. [23]Comai L Tyagi AP Winter K Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids Plant Cell 2000 12 9 1551 1567 11006331 PMC149069
  24. [24]Lee HS Chen ZJ Protein-coding genes are epigenetically regulated in Arabidopsis polyploids Proceedings of the National Academy of Sciences of the United States of America 2001 98 12 6753 6758 11371624 PMC34425
  25. [25]Kashkush K Feldman M Levy AA Gene loss, silencing and activation in a newly synthesized wheat allotetraploid Genetics 2002 160 4 1651 1659 11973318 PMC1462064
  26. [26]Tate JA Ni Z Scheen AC Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid Genetics 2006 173 3 1599 1611 16648586 PMC1526671
  27. [27]Madlung A Masuelli RW Watson B Reynolds SH Davison J Comai L Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids Plant Physiology 2002 129 2 733 746 12068115 PMC161697
  28. [28]Waugh O’Neill RJ O’Neill MJ Marshall Graves JA Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid Nature 1998 393 6680 68 72 9590690
  29. [29]Feldman M Levy AA Allopolyploidy—a shaping force in the evolution of wheat genomes Cytogenetic and Genome Research 2005 109 1–3 250 258 15753584
  30. [31]Feldman M Liu B Segal G Abbo S Levy AA Vega JM Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes Genetics 1997 147 3 1381 1387 9383078 PMC1208259
  31. [32]Khasdan V Yaakov B Kraitshtein Z Kashkush K Developmental timing of DNA elimination following allopolyploidization in wheat Genetics 2010 185 1 387 390 20215467 PMC2870972
  32. [33]Daud HM Gustafson JP Molecular evidence for Triticum speltoides as a B-genome progenitor of wheat (Triticum aestivum) Genome 1996 39 3 543 548 18469915
  33. [35]Salina EA Numerova OM Ozkan H Feldman M Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat Genome 2004 47 5 860 867 15499400
  34. [36]Anamthawat-Jonsson K Heslop-Harrison JS Isolation and characterization of genome-specific DNA sequences in Triticeae species Molecular and General Genetics 1993 240 2 151 158 8355649
  35. [37]Galitski T Saldanha AJ Styles CA Lander ES Fink GR Ploidy regulation of gene expression Science 1999 285 5425 251 254 10398601
  36. [38]Guo M Davis D Birchler JA Dosage effects on gene expression in a maize ploidy series Genetics 1996 142 4 1349 1355 8846910 PMC1207130
  37. [39]Nigumann P Redik K Mätlik K Speek M Many human genes are transcribed from the antisense promoter of L1 retrotransposon Genomics 2002 79 5 628 634 11991712
  38. [40]Vicient CM Jääskeläinen MJ Kalendar R Schulman AH Active retrotransposons are a common feature of grass genomes Plant Physiology 2001 125 3 1283 1292 11244109 PMC65608
  39. [41]Kashkush K Khasdan V 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 2007 177 4 1975 1985 18073417 PMC2219487
  40. [42]Madlung A Tyagi AP Watson B Genomic changes in synthetic Arabidopsis polyploids Plant Journal 2005 41 2 221 230 15634199
  41. [43]Masson P Surosky R Kingsbury JA Fedoroff NV Genetic and molecular analysis of the Spm-dependent a-m2 alleles of the maize a locus Genetics 1987 117 1 117 137 2822531 PMC1203180
  42. [44]Martienssen R Barkan A Taylor WC Freeling M Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize Genes and Development 1990 4 3 331 343 2159936
  43. [45]Puig M Cáceres M Ruiz A Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA Proceedings of the National Academy of Sciences of the United States of America 2004 101 24 9013 9018 15184654 PMC428464
  44. [46]Kraitshtein Z Yaakov B Khasdan V The genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat Genetics 2010 186 801 812 20823338 PMC2975285
  45. [47]Beaulieu J Jean M Belzile F The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants Molecular Genetics and Genomics 2009 281 4 421 435 19148683
  46. [48]Salmon A Ainouche ML Wendel JF Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae) Molecular Ecology 2005 14 4 1163 1175 15773943
  47. [49]Xu Y Zhong L Wu X Fang X Wang J Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids Planta 2009 229 3 471 483 18998158
  48. [50]Lukens LN Pires JC Leon E Vogelzang R Oslach L Osborn T Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids Plant Physiology 2006 140 1 336 348 16377753 PMC1326055
  49. [51]Parisod C Salmon A Zerjal T Tenaillon M Grandbastien MA Ainouche M Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina New Phytologist 2009 184 4 1003 1015 19780987
  50. [52]Yaakov B Kashkush K Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid Genome 2010 54 1 42 49 21217805
  51. [53]Sasakuma T Ogihara Y Tsujimoto H Li Z Xin Z Genome rearrangement of repetitive sequences in processes of hybridization and amphiploidization in Triticinae In: Proceedings of the 8th International Wheat Genetics Symposium 1995 563 566
  52. [54]Petit M Guidat C Daniel J Mobilization of retrotransposons in synthetic allotetraploid tobacco New Phytologist 2010 186 1 135 147 20074093
  53. [55]Bento M Pereira HS Rocheta M Gustafson P Viegas W Silva M Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in triticale PLoS ONE 2008 3 1 Article ID e1402. PMC2151762 18167561
  54. [56]Mestiri I Chagué V Tanguy AM Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity New Phytologist 2010 186 1 86 101 20149116
  55. [57]Parisod C Alix K Just J Impact of transposable elements on the organization and function of allopolyploid genomes New Phytologist 2010 186 1 37 45 20002321
  56. [58]Charles M Belcram H Just J Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat Genetics 2008 180 2 1071 1086 18780739 PMC2567357
  57. [59]Devos KM Brown JKM Bennetzen JL Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis Genome Research 2002 12 7 1075 1079 12097344 PMC186626
  58. [60]Bennetzen JL Ma J Devos KM Mechanisms of recent genome size variation in flowering plants Annals of Botany 2005 95 1 127 132 15596462 PMC4246713
  59. [61]Grover CE Kim H Wing RA Paterson AH Wendel JF Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium) Plant Journal 2007 50 6 995 1006 17461788
  60. [62]Wicker T Guyot R Yahiaoui N Keller B CACTA transposons in triticeae. A diverse family of high-copy repetitive elements Plant Physiology 2003 132 1 52 63 12746511 PMC166951
  61. [63]Chantret N Salse J Sabot F Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops) Plant Cell 2005 17 4 1033 1045 15749759 PMC1087984
  62. [64]Feldman M Levy AA Allopolyploidy—a shaping force in the evolution of wheat genomes Cytogenetic and Genome Research 2005 109 1-3 250 258 15753584

Cited by

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Authors
Yaakov, B., & Kashkush, K.
Affiliations
Ben-Gurion University of the Negev (IL)
Corresponding author
Kashkush, Khalil
ORCID
Venue
International Journal of Plant Genomics
Publisher
Wiley
Published
2011-05-15
Volume
2011
Pages
1-7
ISSN
  • 1687-5370 (ISSN-L)
  • 1687-5389
DOI
10.1155/2011/569826
PMC
PMC3134107
OpenAlex
W2074879186
Cited by
51
References
0
Citations by year
2024: 1 · 2023: 4 · 2022: 4 · 2021: 1 · 2020: 3 · 2019: 2 · 2018: 3 · 2017: 1 · 2016: 4 · 2015: 5 · 2014: 8 · 2013: 7 · 2012: 7
FWCI
8.87
Type
journal article
Language
en
Open access
Licence
Locations
  • International Journal of Plant Genomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
Israel Science Foundation (142/08)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Wheat and Barley Genetics and Pathology
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Taxonomy and Phylogenetics
Keywords
transposable elements, allopolyploidization, DNA methylation, epigenetic regulation, transposon transcription, wheat, allohexaploid wheat, genome rearrangement, hybridity

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