Genomes contain more than the DNA sequences that directly support an organism’s functions. Many also include transposable elements, or “jumping genes,” which can copy and insert themselves into new locations. Their activity can substantially increase genome size, although the evolutionary reasons behind these changes remain unclear.
Researchers at The Ohio State University created PrinTE to study that history. The simulator starts from an inferred ancestral genome and models how insertions and deletions could have produced a modern genome. It builds on an earlier tool, TEGenomeSimulator, which provided a snapshot of transposon activity at a single point in time.
The team tested PrinTE using fungal genomes, focusing on the subdivision that includes myrtle rust. That fungus has a genome of about 1 billion base pairs, an unusually large size for fungi, largely because of transposon insertions. Researchers reconstructed a theoretical common ancestor and ran simulations to identify evolutionary paths that could lead to the present-day genome.
Because the simulations span millions of generations, PrinTE uses machine learning to identify trajectories moving away from plausible outcomes and stop them. Researchers may need thousands of simulations before finding one that best matches the modern genome, allowing them to test different hypotheses about past transposon activity.
The myrtle rust case study indicated that the insertion rate was four to five times higher than the deletion rate. These bursts of activity were followed by a decline in insertions, suggesting that the host eventually developed stronger control over the transposable elements and began removing some of them.
The findings also relate to the genome size paradox: organisms with significantly different genome sizes can nevertheless perform similar functions. The corn genome, for example, is reported to contain transposable elements across as much as 85% of its DNA. These elements can increase genome size through repeated copy-and-paste events without necessarily producing a correspondingly more complex organism.
The researchers said PrinTE could provide a framework for examining transposon evolutionary histories in other organisms. The publicly available tool has already been used to study additional systems. The work was published in Nature Communications on Nov. 2, 2026, under the title “PrinTE: a forward simulation framework for studying the role of transposable elements in genome expansion and contraction.”
Sources: Phys.org.