Transposable elements: Drivers of regulatory innovation and adaptation in plants

Abstract

Transposable elements (TEs) constitute a major fraction of eukaryotic genomes and represent one of the most abundant classes of repetitive sequences in plants. Recent advances in sequencing technologies, together with the increasing availability of telomere-to-telomere and pan-genome assemblies, have enabled comprehensive characterization of TE sequences, revealing their complex architectures, structural variation, and evolutionary dynamics across diverse plant species. Because TE mobilization can compromise gene function and genome integrity, plants have evolved sophisticated epigenetic mechanisms to restrict TE activity. In turn, TEs have co-evolved diverse strategies to evade host silencing, reflecting a continuous evolutionary arms race between host genomes and their mobile elements. Beyond their traditional view as genomic parasites, accumulating evidence now demonstrates that TEs are major drivers of genome innovation by providing novel protein-coding modules, cis -regulatory elements, and structural variation that reshape chromatin organization and gene regulatory networks. In this review, we highlight recent advances in our understanding of how TEs promote regulatory innovation, environmental adaptation, and genome evolution in plants.