Haplotype‐resolved telomere‐to‐telomere genome assembly of Populus lasiocarpa unveils retrotransposon‐driven centromere evolution

SUMMARY Centromeres, essential for chromosome segregation, exhibit remarkable evolutionary dynamism in sequence composition and structural organization. Here, we report the first haplotype‐resolved, telomere‐to‐telomere genome assembly of Populus lasiocarpa (PLAS) and precisely map all 38 functional centromeres through CENH3 ChIP‐Seq. Unlike classical satellite‐rich centromeres in model plants, PLAS centromeres lack abundant satellite arrays but are dominated by retrotransposons, particularly RLG and RIL elements, which form intricate nested TE arrays within the functional centromeric regions, disrupting their structural integrity and driving their evolution. Comparative analysis with P. trichocarpa reveals a conserved retrotransposon‐dominated architecture, despite minimal sequence conservation. We propose a cyclic model of centromere evolution in which autonomous retrotransposons destabilize functional centromeres through epigenetic erosion, triggering neocentromere formation at pericentromeric sites enriched in transposable elements (TEs) and tandem repeats (TRs). These neocentromeres either succumb to recurrent retrotransposon invasions or stabilize through KARMA‐mediated TR expansion, ultimately giving rise to satellite‐rich centromeres. Our work redefines centromeres as dynamic, epigenetically plastic domains shaped by retrotransposon‐TR antagonism, challenging the satellite‐centric paradigm and offering novel insights into plant genome evolution.