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. 1. Introduction Some DNA sequences possess the unique ability to move from one place in the genome to another, these sequences are usually termed transposable elements (TEs). TEs makeup a large fraction of most eukaryotic genomes, particularly grasses, where they occupy up to 90% of the genome [1]. TEs are classified into two main groups, based on the intermediate molecule that mediates their movement: (1) RNA elements (retrotransposons or class 1 transposons) have RNA as their intermediate molecule; and (2) DNA elements (class 2 transposons) have DNA as their intermediate molecule [2]. TEs are considered “parasitic”, as the success of their reproduction is negatively correlated with the fitness of the host organism [3]. Some TEs have a marked preference for insertion within or near the vicinity of genes [4]. TE transposition can cause chromosome breakage, illegitimate recombination and genome rearrangement [3]. In addition, TEs can also affect gene expression if positioned into or near the gene [5–7]. In order to control their activity, TEs are mostly heavily methylated by the host, and as such, are associated with heterochromatin [3]. The bias of methylation toward repetitive DNA suggests that silencing of transposable elements is one of the primary roles of DNA methylation [8]. The Arabidopsis genome contains 24% methylated CG sites, 6.7% methylated CHG sites (H = A, C or T) and 1.7% methylated CHH sites [9]. The entire sequence of transposable elements is usually methylated in Arabidopsis, in all sequence contexts [8]. Considering that DNA demethylation or hypermethylation of transposable element sequences is
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