Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization

Plant Cell Reports

Volumn 32, Issue 10, 2013, Pages 1615-1624

  Yaakov, Beery ^a   Meyer, Karin ^a   Ben David, Smadar ^a   Kashkush, Khalil ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

Copy number variation; Genome evolution; Speciation; Transposable elements; Wheat

Indexed keywords

PLANT DNA;

ARTICLE; CLASSIFICATION; COPY NUMBER VARIATION; GENETICS; MOLECULAR EVOLUTION; PLANT GENOME; POLYPLOIDY; SPECIES DIFFERENCE; TRANSPOSON; WHEAT;

DNA COPY NUMBER VARIATIONS; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; EVOLUTION, MOLECULAR; GENOME, PLANT; POLYPLOIDY; SPECIES SPECIFICITY; TRITICUM;

AEGILOPS; TRITICUM; TRITICUM AESTIVUM;

EID: 84884204399     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-013-1472-8     Document Type: Article

References (56)

1. Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8: 135-141.
2. Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB (2010) Annotating non-coding regions of the genome. Nat Rev Genet 11: 559-571.
3. Asakura N, Yoshida S, Mori N, Ohtsuka I, Nakamura C (2008) Sequence diversity and copy number variation of Mutator-like transposases in wheat. Genet Mol Biol 31: 539-546.
4. Baruch O, Kashkush K (2012) Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains. Plant Cell Rep 31: 885-893.
5. Bento M, Pereira HS, Rocheta M, Gustafson P, Viegas W, Silva M (2008) Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in Triticale. PLoS One 3: 1402.
6. Bleykasten-Grosshans C, Jung PP, Fritsch SE, Potier S, Montigny Jd, Souciet JL (2011) TheTy1LTR-retrotransposon population in Saccharomyces cerevisiae genome: dynamics and sequence variations during mobility. FEMS Yeast Res 11: 334-344.
7. Brenchley R et al (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491: 705-710.
8. Cantu D, Vanzetti L, Sumner A, Dubcovsky M, Matvienko M, Distelfeld A, Michelmore R, Dubcovsky J (2010) Small RNAs, DNA methylation and transposable elements in wheat. BMC genomics 11: 408.
9. Charles M, Belcram H, Just J, Huneau C, Viollet A, Couloux A, Segurens B, Carter M, Huteau V, Coriton O (2008) Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 180: 1071.
10. Chen ZJ (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol 58: 377-406.
11. Comai L (2005) The advantages and disadvantages of being polyploid. Nat Rev Genet 6: 836-846.
12. Deininger PL, Batzer MA (2002) Mammalian Retroelements. Genome Res 12: 1455-1465.
13. Devos KM, Brown JKM, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075.
14. Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316: 1862-1866.
15. Feldman M, Levy AA (2005) Allopolyploidy-a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109: 250-258.
16. Feldman M, Levy AA (2009) Genome evolution in allopolyploid wheat-a revolutionary reprogramming followed by gradual changes. J Gene Genomics 36: 511-518 (Yi chuan xue bao).
17. Grandbastien M, Audeon C, Bonnivard E, Casacuberta JM, Chalhoub B, Costa APP, Le QH, Melayah D, Petit M, Poncet C, Tam SM, van Sluys MA, Mhiri C (2005) Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res 110: 229-241.
18. Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH (2011) Retrotransposition of marked SVA elements by human L1 s in cultured cells. Hum Mol Genet 20: 3386-3400.
19. Hosid E, Brodsky L, Kalendar R, Raskina O, Belyayev A (2012) Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides. Genetics 190: 263-274.
20. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol 3: RESEARCH0084.
21. Kashkush K, 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: 1975-1985.
22. Kashkush K, Feldman M, Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33: 102-106.
23. Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, Levy AA (2011) Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 188: 263-272.
24. Kraitshtein Z, Yaakov B, Khasdan V, Kashkush K (2010) The genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 186: 801-812.
25. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532.
26. Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
27. Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60: 43-66.
28. Liu B, Vega JM, Feldman M (1998) Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 41: 535-542.
29. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 25: 402-408.
30. Ma XF, Fang P, Gustafson JP (2004) Polyploidization-induced genome variation in triticale. Genome 47: 839-848.
31. Mansour A (2007) Epigenetic activation of genomic retrotransposons. J Cell Mol Biol 6: 99-107.
32. Mirouze M, Lieberman-Lazarovich M, Aversano R, Bucher E, Nicolet J, Reinders J, Paszkowski J (2012) Loss of DNA methylation affects the recombination landscape in Arabidopsis. Proc Natl Acad Sci 109: 5880-5885.
33. Ozkan H, Levy AA, Feldman M (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13: 1735-1747.
34. Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184: 1003-1015.
35. Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B, Grandbastien MA (2010) Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186: 37-45.
36. Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui QT, Lim KY, Kovarik A, Leitch AR, Grandbastien M (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186: 135-147.
37. Puig M, Cáceres M, Ruiz A (2004) Silencing of a gene adjacent to the breakpoint of a widespread Drosophila inversion by a transposon-induced antisense RNA. Proc Natl Acad Sci USA 101: 9013-9018.
38. Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Genet Genomics 271: 91-97.
39. Sabot F, Guyot R, Wicker T, Chantret N, Laubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M (2005) Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics 274: 119-130.
40. Salina E, Sergeeva E, Adonina I, Shcherban A, Belcram H, Huneau C, Chalhoub B (2011) The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. BMC Plant Biol 11: 1-14.
41. Salse J, Chague V, Bolot S, Magdelenat G, Huneau C, Pont C, Belcram H, Couloux A, Gardais S, Evrard A, Segurens B, Charles M, Ravel C, Samain S, Charmet G, Boudet N, Chalhoub B (2008) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC genomics 9: 555.
42. Schnable PS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
43. Senerchia N, Wicker T, Felber F, Parisod C (2013) Evolutionary dynamics of retrotransposons assessed by high throughput sequencing in wild relatives of wheat. Genome Biol Evol 5: 1010-1020.
44. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-1759.
45. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
46. Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15: 471-478.
47. Tomita M, Shinohara K, Morimoto M (2008) Revolver is a new class of transposon-like gene composing the Triticeae genome. DNA Res 15: 49-62.
48. Wicker T, Sabot F, Hua-van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982.
49. Wright S, Schoen D (2000) Transposon dynamics and the breeding system. In: McDonald J (ed) Transposable elements and genome evolution. Springer, Netherlands, pp 139-148 vol [107(1-3)].
50. Xuan YH, Zhang J, Peterson T, Han CD (2012) Ac/Ds-induced chromosomal rearrangements in rice genomes. Mob Genet Elements 2: 67-71.
51. Yaakov B, Kashkush K (2011a) Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid. Genome 54: 42-49.
52. Yaakov B, Kashkush K (2011b) Methylation, Transcription, and Rearrangements of transposable elements in synthetic allopolyploids. International journal of plant genomics 2011.
53. Yaakov B, Kashkush K (2012) Mobilization of Stowaway-like MITEs in newly formed allohexaploid wheat species. Plant Mol Biol. doi: 10. 1007/s11103-11012-19957-11103.
54. Yaakov B, Ben-David S, Kashkush K (2013) Genome-wide analysis of Stowaway-like MITEs in wheat revealed high sequence conservation, association with genes and genomic diversification. Plant Physiol 1: 486-496.
55. Yaakov B, Ceylan E, Domb K, Kashkush K (2012) Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution. Theor Appl Genet 7: 1-9.
56. Zhao N, Zhu B, Li M, Wang L, Xu L, Zhang H, Zheng S, Qi B, Han F, Liu B (2011) Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat. Genetics 188: 499-510.