A segmental duplication-mediated deletion leads to neocentromere formation in orangutans
Centromeres ensure faithful chromosome segregation, yet how new centromeres arise and replace canonical ones remains poorly understood. Here, we investigate a polymorphic centromere repositioning event on the orangutan chromosome 10 using near-telomere-to-telomere assemblies, epigenetic profiling, and population-scale data. We identify striking heterogeneity in canonical centromeres, ranging from large, higher-order repeat α-satellite arrays to short, monomeric α-satellite tracts, alongside the emergence of neocentromeres lacking α-satellite DNA. We show a segmental duplication-mediated deletion of 3.6 Mbp that removed the higher-order repeat array, promoting centromere repositioning and neocentromere formation. Phylogenetic analyses reveal complex evolutionary dynamics, including introgression and incomplete lineage sorting in orangutan lineages. These findings demonstrate that centromere identity can evolve through structural variation and epigenetic reprogramming, highlighting its remarkable plasticity in primate genomes.
Authors
- Francesco Montinaro (ORCID: https://orcid.org/0000-0002-4506-963X)
- Glennis A. Logsdon (ORCID: https://orcid.org/0000-0003-2396-0656)
- Francesco Ravasini (ORCID: https://orcid.org/0000-0003-2866-5533)
- Beniamino Trombetta (ORCID: https://orcid.org/0000-0001-8245-9437)
- Evan E. Eichler (ORCID: https://orcid.org/0000-0002-8246-4014)
- Luciana de Gennaro (ORCID: https://orcid.org/0009-0007-9572-7630)
- Letizia Pistacchia
- Daan Noordermeer (ORCID: https://orcid.org/0000-0002-9296-7002)
- Fabio Marroni (ORCID: https://orcid.org/0000-0002-1556-5907)
- Alessia Daponte (ORCID: https://orcid.org/0009-0000-1677-8333)
- Cesare Polano (ORCID: https://orcid.org/0000-0001-5612-9856)
- Kendra Hoekzema (ORCID: https://orcid.org/0000-0002-8058-0177)
- Mario Ventura (ORCID: https://orcid.org/0000-0001-7762-8777)
- Francesca Antonacci (ORCID: https://orcid.org/0000-0002-5833-6186)
- Claudia Rita Catacchio (ORCID: https://orcid.org/0000-0002-2166-723X)
- DongAhn Yoo (ORCID: https://orcid.org/0000-0003-0033-3721)
- Katherine M. Munson (ORCID: https://orcid.org/0000-0001-8413-6498)
- Keisuke K. Oshima (ORCID: https://orcid.org/0009-0002-2229-8998)
- Rosaria Magrone
- Julie Wertz (ORCID: https://orcid.org/0009-0000-3747-3221)
- Kumara F Mastrorosa (ORCID: https://orcid.org/0000-0003-0579-1895)
Institutions
- University of Udine (IT)
- Centre National de la Recherche Scientifique (FR)
- Howard Hughes Medical Institute (US)
- University of Washington (US)
- Aarhus University (DK)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Université Paris-Saclay (FR)
- Institut de Biologie Intégrative de la Cellule (FR)
- CEA Paris-Saclay (FR)
- University of Bari Aldo Moro (IT)
- University of Tartu (EE)
- University of Pennsylvania (US)
- Sapienza University of Rome (IT)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-04-11
- DOI
- https://doi.org/10.64898/2026.04.09.717302
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- European Commission
- National Institutes of Health