The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.