Transposable Elements and Genome Evolution in Vertebrates

Transposable elements (TEs) are pervasive genomic components that have profoundly influenced vertebrate genome evolution. Once regarded as junk DNA, TEs are now recognized as dynamic agents of genetic innovation, shaping genome architecture and gene regulation, while their hyperactivity and aberrant expression can contribute to the onset and progression of various diseases. This chapter provides an overview of TE classification, structure, and transposition mechanisms, highlighting their intra- and interspecies transmission through vertical inheritance and horizontal transfer (HT). We explain the evolutionary forces that shape the fate of TE insertions, their contribution to expanding genomic diversity, and their capacity to drive functional and regulatory innovations. We emphasize TE-mediated exonization, gene duplication, cis- and trans-regulatory effects, and their impact on evolutionary divergence and speciation. We also discuss the coevolutionary “arms race” between TEs and host genomes, detailing silencing mechanisms and TE counterstrategies. Ultimately, we explore how TE-driven genome expansion and contraction govern genome size dynamics under the “accordion model” and outline emerging research frontiers enabled by long-read sequencing, single-cell technologies, and comparative genomics. Altogether, TEs are not merely relics of past invasions but central architects of genome plasticity, innovation, and evolutionary adaptation in vertebrates.