Rare transposable elements challenge the prevailing view of transposition dynamics in plants

Transposable elements (TEs) in plants are best known for their ability to inflate genome size and their potential effects on host phenotypes. In this essay, we suggest that many TEs do none of these things, but survive and replicate inconspicuously in the host genome. Transposable elements are frequently depicted as “invasive” sequences with a tendency to replicate in “bursts” as soon as the silencing mechanisms keeping them in check are relaxed. While massive amplifications do occur and have intriguing consequences, this way of thinking about TEs, guided by analogies from horizontally transmitted pathogens, can be misleading. By means of the example of Alesia elements—a retrotransposon lineage present at low copy numbers throughout angiosperms—we propose a scenario of vertical descent in which TEs are maintained in evolution not because of their ability to invade and amplify, but because they have evolved strategies to persist at low copy numbers. Studying the adaptive traits of rare TEs across species promises intriguing insights into the world of intragenomic conflict and a more nuanced view of transposition dynamics in plants