Parida, A. C. | bioRxiv Science

bioRxiv2026

The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis

Centromeres are critical for accurate segregation of chromosomes and are often composed of megabases of tandemly arranged satellite repeats. Yet, despite their conserved function, the DNA sequence of centromeres is, paradoxically, rapidly evolving. To understand the nature of centromeric sequence turnover, we assembled 417 centromeres from nine species representing the entire Arabidopsis genus. In the genus, centromeres are formed by four main satellite repeats with homologous sequences forming central arrays and minor repeat types. We identify the ancestral centromeric repeat type for the Arabidopsis genus and three independent turnovers to different repeats: (1) a complete turnover in A. thaliana, (2) a turnover of seven out of the eight centromeres in the ancestor of A. cebennensis and A. pedemontana, (3) turnovers of three to five centromeres in the genomes of A. halleri and A. lyrata. Most centromeric repeats are also present throughout the genome with shared syntenic locations between Arabidopsis species, and some being similar to parts of transposable elements and genes, suggesting that centromeric repeats originate outside of the centromeres. In allotetraploid A. suecica we find that the repeats from centromeric arrays on one subgenome can transpose and invade the other, likely via transposable element activity. All four main centromeric repeats can recruit the CENH3 (CENP-A) histone variant, however, when a new repeat successfully proliferates in an old array, CENH3 is primarily recruited to the new array marking functional take over. Complete centromeric turnovers occurred in species that experienced severe bottlenecks in their evolutionary history, where new centromeric alleles may have been fixed by genetic drift. Yet, we also observe segregation distortion between two different centromeric repeat types in A. lyrata, suggestive of centromere drive and we propose that both drift and drive contribute to centromeric repeat turnover. Together, our findings reveal the origin of centromeric repeats, mechanisms of repeat proliferation and spread, and the evolutionary dynamics of centromeric repeat turnovers in the Arabidopsis genus.

evolutionary biology↗

bioRxiv2025

Interlocus gene conversion causes mosaic divergence in tandem paralogues - simulating HMA4 evolution in Arabidopsis halleri

Following gene duplication, the evolutionary trajectories of gene copies can be shaped by various processes including mutation, selection, recombination and interlocus gene conversion (IGC). To explore their dynamics and consequences, we developed a mathematical model that simulates the early evolution of recently duplicated, tandemly arrayed gene families with positive selection on the new gene copy. We compared the results of our model to sequence variation of the three tandemly arrayed HEAVY METAL ATPase 4 (HMA4) gene copies of Arabidopsis halleri, which are known to undergo IGC. However, rate and efficacy of IGC vary within genes, resulting in a mosaic pattern of divergence. Informed by empirical data, our model captures the impact of IGC and unequal crossing-over on the diversity within each gene copy and the divergence among them. By tailoring the model to the HMA4 gene copies, we demonstrate the models flexibility and its potential to provide insights into the evolutionary dynamics driving the evolution of tandemly arrayed paralogues. This study enhances our understanding of the balance between homogenization and divergence of gene family evolution.

evolutionary biology↗