Yuhong Huang#, Chuanye Chen#, Xin Wang#, Yiqian Chen, Jingwei Zhou, Jianwei Zhang, Martin A. Lysak, Handong Su*

Molecular Plant, December 17, 2025

Abstract

Centromeres are indispensable for accurate chromosome segregation, but are subject to rapid sequence turnover while maintaining conserved functions –– a paradox in genome evolution. To unravel this paradox, we integrated over 400 fully resolved centromeres from 17 diploid angiosperms spanning 180 million years of divergence, along with 1,000+ pan-genomic assemblies, resequencing datasets, and congeneric whole-genome sequences. Our study shows that angiosperm centromere organization is determined by lineage-specific combinations of satellite repeat and transposable element (TE), which in turn shape distinct epigenetic landscapes and evolutionary trajectories within centromeres. In particular, TE insertion patterns are found to be one key driver of structural diversification and positional shift of centromeres in angiosperms. Intriguingly, population-level analyses uncovered considerable plasticity in centromere sequences within species, with satellite repeats acting as focal points of evolutionary change and displaying species-specific heterogeneity patterns. Temporal reconstructions across congeneric species revealed the emergence and subsequent differentiation of centromeric repeats, outlining a dynamic continuum from gradual sequence diversification to complete turnover during speciation over time, often accompanied by karyotype reorganization. By integrating intra- and inter-species comparisons, we propose a unifying framework in which centromere innovation is governed by a delicate interplay between genome evolution, chromosomal shuffling and selection constraints, resulting in phylogenomic signatures of centromere-driven speciation.

Keywords

centromere evolution; angiosperm plants; CENH3; satellite; transposable elements; speciation

论文链接：https://www.cell.com/molecular-plant/fulltext/S1674-2052(25)00444-7