Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid

Genome

Volumn 54, Issue 1, 2010, Pages 42-49

  Yaakov, Beery ^a   Kashkush, Khalil ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

cytosine methylation; genome evolution; polyploidy; transposable elements; wheat

Indexed keywords

ARTICLE; DNA METHYLATION; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MOLECULAR EVOLUTION; PLANT CHROMOSOME; PLANT GENOME; POLYPLOIDY; SPECIES DIFFERENTIATION; TRANSPOSON; WHEAT;

CHROMOSOMES, PLANT; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; GENETIC SPECIATION; GENOME, PLANT; POLYPLOIDY; TRITICUM;

TRITICUM AESTIVUM;

EID: 78651388093     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G10-091     Document Type: Article

References (33)

1. Adams, K.L., and Wendel, J.F. 2005. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8 (2): 135-141. 10.1016/j.pbi.2005.01.001 15752992 (Pubitemid 40323541)
2. Beaulieu, J., Jean, M., and Belzile, F. 2009. The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants. Mol. Genet. Genomics, 281 (4): 421-435. 10.1007/s00438-008-0421-7 19148683
3. Bento, M., Pereira, H.S., Rocheta, M., Gustafson, P., Viegas, W., Silva, M., and Fraser, J. 2008. Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in Triticale. PLoS One, 3 (1): e1402. 10.1371/journal.pone.0001402 (Pubitemid 351194014)
4. Capy, P., Gasperi, G., Biémont, C., and Bazin, C. 2000. Stress and transposable elements: co-evolution or useful parasites? Heredity, 85 (2): 101-106. 10.1046/j.1365-2540.2000.00751.x 11012710
5. Chen, M., Ha, M., Lackey, E., Wang, J.L., and Chen, Z.J. 2008. RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics, 178 (4): 1845-1858. 10.1534/genetics.107.086272 18430920
6. Comai, L., Madlung, A., Josefsson, C., and Tyagi, A. 2003. Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids? Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (1434): 1149-1155. 10.1098/rstb.2003.1305 12831481 (Pubitemid 36774908)
7. Feldman, M., and Levy, A.A. 2005. Allopolyploidy a shaping force in the evolution of wheat genomes. Cytogenet. Genome Res. 109 (1-3): 250-258. 10.1159/000082407 15753584 (Pubitemid 40470330)
8. Feschotte, C., and Pritham, E.J. 2007. Transposons and the evolution of eukaryotic genomes. Annu. Rev. Genet. 41: 331-368. 18076328
9. Grandbastien, M.A., Audeon, C., Bonnivard, E., Casacuberta, J.M., Chalhoub, B., Costa, A.P.P., et al. 2005. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110 (1-4): 229-241. 10.1159/000084957 16093677 (Pubitemid 41159902)
10. Kashkush, K., and 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 (4): 1975-1985. 10.1534/genetics.107.080234 18073417 (Pubitemid 350276981)
11. Kashkush, K., Feldman, M., and Levy, A.A. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics, 160 (4): 1651-1659. 11973318
12. Kashkush, K., Feldman, M., and Levy, A.A. 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33 (1): 102-106. 10.1038/ng1063 12483211 (Pubitemid 36068691)
13. Khasdan, V., Yaakov, B., Kraitshtein, Z., and Kashkush, K. 2010. Developmental timing of DNA elimination following allopolyploidization in wheat. Genetics, 185 (1): 387-390. 10.1534/genetics.110.116178 20215467
14. Lackey, E., Ng, D.W.K., and Chen, Z.J. 2010. RNAi-mediated down-regulation of DCL1 and AGO1 induces developmental changes in resynthesized Arabidopsis allotetraploids. New Phytol. 186 (1): 207-215. 10.1111/j.1469-8137. 2010.03187.x 20409179
15. Levy, A.A., and Feldman, M. 2004. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biol. J. Linn. Soc. 82 (4): 607-613. 10.1111/j.1095-8312.2004.00346.x (Pubitemid 39123347)
16. Liu, B., Vega, J.M., and Feldman, M. 1998 a. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome, 41 (4): 535-542. 10.1139/gen-41-4-535 9796102 (Pubitemid 28532091)
17. Liu, B., Vega, J.M., Segal, G., Abbo, S., Rodova, H., and Feldman, M. 1998 b. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences. Genome, 41 (2): 272-277. 10.1139/gen-41-2-272 (Pubitemid 28370090)
18. Lynch, M., and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science, 290 (5494): 1151-1155. 10.1126/science.290.5494. 1151 11073452
19. Madlung, A., Masuelli, R.W., Watson, B., Reynolds, S.H., Davison, J., and Comai, L. 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129 (2): 733-746. 10.1104/pp.003095 12068115 (Pubitemid 34689159)
20. Madlung, A., Tyagi, A.P., Watson, B., Jiang, H.M., Kagochi, T., Doerge, R.W., et al. 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 41 (2): 221-230. 10.1111/j.1365-313X.2004.02297.x 15634199 (Pubitemid 40162248)
21. Mestiri, I., Chagué, V., Tanguy, A.M., Huneau, C., Huteau, V., Belcram, H., et al. 2010. Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol. 186 (1): 86-101. 10.1111/j.1469-8137.2010.03186.x 20149116
22. Ozkan, H., Levy, A.A., and Feldman, M. 2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell, 13 (8): 1735-1747. 10.1105/tpc.13.8.1735 11487689 (Pubitemid 32781987)
23. Parisod, C., Salmon, A., Zerjal, T., Tenaillon, M., Grandbastien, M.A., and Ainouche, M. 2009. Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol. 184 (4): 1003-1015. 10.1111/j.1469-8137.2009.03029.x 19780987
24. Parisod, C., Alix, K., Just, J., Petit, M., Sarilar, V., Mhiri, C., et al. 2010. Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol. 186 (1): 37-45. 10.1111/j.1469-8137.2009. 03096.x 20002321
25. Petit, M., Guidat, C., Daniel, J., Denis, E., Montoriol, E., Bui, Q.T., et al. 2010. Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol. 186 (1): 135-147. 10.1111/j.1469-8137.2009.03140.x 20074093
26. Salmon, A., Ainouche, M.L., and Wendel, J.F. 2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 14 (4): 1163-1175. 10.1111/j.1365-294X.2005.02488.x 15773943 (Pubitemid 40466242)
27. Shaked, H., Kashkush, K., Ozkan, H., Feldman, M., and Levy, A.A. 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell, 13 (8): 1749-1759. 10.1105/tpc.13.8.1749 11487690 (Pubitemid 32781988)
28. Skalick, K., Lim, K.Y., Matyasek, R., Matzke, M., Leitch, A.R., and Kovarik, A. 2005. Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytol. 166 (1): 291-303. 10.1111/j.1469-8137.2004.01297.x 15760371 (Pubitemid 40428153)
29. Slotkin, R.K., and Martienssen, R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8 (4): 272-285. 10.1038/nrg2072 17363976 (Pubitemid 46439291)
30. Stebbins, G.L.J. 1971. Chromosomal evolution in higher plants. Addison-Wesley, New York.
31. Wessler, S.R. 1996. Plant retrotransposons: turned on by stress. Curr. Biol. 6 (8): 959-961. 10.1016/S0960-9822(02)00638-3 8805314 (Pubitemid 26350714)
32. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., et al. 2007. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8 (12): 973-982. 10.1038/nrg2165 17984973 (Pubitemid 350129169)
33. Xu, Y.H., Zhong, L., Wu, X.M., Fang, X.P., and Wang, J.B. 2009. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta, 229 (3): 471-483. 10.1007/s00425-008- 0844-8 18998158