Where the Wild Things Are: Transposable Elements as Drivers of Structural and Functional Variations in the Wheat Genome

Abstract

Transposable elements (TEs) are major contributors to genome plasticity and thus are likely to have a dramatic impact on genetic diversity and speciation. Recent technological developments facilitated the sequencing and assembly of the wheat genome, opening the gate for whole genome analysis of TEs in wheat, which occupy over 80% of the genome. Questions that have been long unanswered regarding TE dynamics throughout the evolution of wheat, are now being addressed more easily, while new questions are rising. In this review, we discuss recent advances in the field of TE dynamics in wheat and possible future directions.

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

“…Most, if not all, TEs can also replicate host sequences [125], so structural variation arising from TEs can be diverse in origin, and due to the myriad of replicative mechanisms among TEs, diverse in form. While typified by insertion-deletion events, TE-associated structural variation commonly includes inversions and can be a source of copy number variations, large deletions, duplications, and translocations [126][127][128]. Beyond these basics, TE-associated structural variation is best understood in the context of specific TE types and their lifecycles.…”

Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes

“…tauschii genotypes. Types and abundances of repetitive DNA might have an impact on the expression of the adjacent genes ( Ramírez-González et al, 2018 ; Bariah et al, 2020 ). TEs also have an impact on DNA methylation and expression of nearby genes in the different plant species ( Makarevitch et al, 2015 ; Wang et al, 2018 ; Stritt et al, 2020 ).…”

Evolution of Diverse Strategies for Promoter Regulation

“…Significantly, active transposable elements can increase the size of the genome and facilitate rapid genetic adaptation to stressful environments [88]. Transposition activity can have positive and negative influences on gene expression and strong promoters from viruses and transposable elements contribute to the rapid genetic diversity of primates [89] and many plant species [90,91]. It is also of note that stable and conserved G-quadruplexes are located in the long terminal repeat (LTR) promoter of retroviruses [92] and human herpesviruses immediate-early promoters [58].…”