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

PrinTE, a forward-time whole-genome simulator, recovers transposon insertion and deletion rates with <6% error across simulations spanning four orders of magnitude.

• Why it matters: Genome expansion and contraction are linked to transposable element activity, but the dynamics are hard to infer without historical records of genome change.
• What they did: PrinTE simulates whole-genome sequences with customizable transposon dynamics and fits evolutionary parameters to an observed genome, including applications to Arabidopsis and Pucciniomycotina such as Austropuccinia psidii.
• The result: For Austropuccinia psidii, genome expansion to 1,018 Mb is linked to transposon amplifications, and simulations suggest recombination-based removal of LTR retrotransposons alone cannot prevent genome obesity.

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