The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis
- 1Max Planck Institute for Plant Breeding Research
Abstract
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.
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BibTeX
@misc{glushkevich2026nature,
title = {{The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis}},
author = {A. Glushkevich and R. Burns and M. Vasilarou and E. Perez-Roman and U. Kolesnikova and A. C. Parida and L. A. Robledillo and A. Mackintosh and R. Suda and L. Steinmann and U. Pfordt and K. Schmid and U. Kraemer and A. Marques and T. Tsuchimatsu and T. M. Mattila and A. Bousios and I. Henderson and A. D. Scott and P. Y. Novikova},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.10.749358},
url = {https://www.biorxiv.org/content/10.64898/2026.09.10.749358v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis
AU - A. Glushkevich
AU - R. Burns
AU - M. Vasilarou
AU - E. Perez-Roman
AU - U. Kolesnikova
AU - A. C. Parida
AU - L. A. Robledillo
AU - A. Mackintosh
AU - R. Suda
AU - L. Steinmann
AU - U. Pfordt
AU - K. Schmid
AU - U. Kraemer
AU - A. Marques
AU - T. Tsuchimatsu
AU - T. M. Mattila
AU - A. Bousios
AU - I. Henderson
AU - A. D. Scott
AU - P. Y. Novikova
PY - 2026
DA - 2026/09/10
PB - bioRxiv
DO - 10.64898/2026.09.10.749358
UR - https://www.biorxiv.org/content/10.64898/2026.09.10.749358v1
AB - 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.
ER -