PrinTE: a forward simulation framework for studying the role of transposable elements in genome expansion and contraction

Genome expansion and contraction are driven by transposable element activity, but the underlying dynamics remain enigmatic due to a lack of historical records tracing these changes. Here, we present PrinTE, a forward-time simulator of whole-genome sequences with customizable transposon dynamics for identifying the evolutionary parameters most consistent with an observed genome. Across simulations spanning four orders of magnitude, PrinTE recovers transposon insertion and deletion rates with less than 6% error. We demonstrate PrinTE on Arabidopsis and the fungal subdivision Pucciniomycotina, including myrtle rust (Austropuccinia psidii), which expanded its genome size to 1,018 Mb through transposon amplifications. Our simulations show that recombination-based removal of LTR retrotransposons alone cannot prevent genome obesity, and that preventing their invasion in the first place is more effective. We hypothesize that A. psidii might have experienced a prolonged expansion phase followed by a potent and ongoing period of contraction.