Transposable elements control gene structure and function in wheat

During the last decade, rapid technological developments have facilitated the sequencing and assembly of the wheat genome, opening the gate for whole-genome analysis of transposable elements (TEs) in wheat, which occupies over 80% of the genome. Recent studies in wheat emphasized the importance of TEs as a major source of intraspecific genetic variation due to their recent activity and involvement in genomic rearrangements. As the major component of the wheat genome, it is now clear that TEs take place in different structural and functional variations of the genome. However, there is still a lot to learn about TE dynamics in wheat genomes and the involving mechanisms. Here we have utilized TEs to study structural variations and their underlying molecular mechanism(s), including insertions/deletions (indels) of large DNA fragments (up to several million bases) between wheat allopolyploid species. In addition, we analyzed tens of RNA-Seq databases to have a better look on the impact of TE insertions within gene bodies on genetic polymorphism and homoeologous gene expression variation in ten sequenced bread wheat lines. To this end, our data indicate that TEs might play a prominent role on wheat speciation.