Evolutionary dynamics of the pan-centromere architecture in oaks
Centromeres ensure faithful chromosome segregation and genome stability, yet their DNA evolves rapidly, presenting a long-standing centromere paradox. Here we characterise the genomic and epigenomic architecture of >1,300 candidate centromeres from 111 high-quality Quercus (oak) genomes. We show that lineage-specific expansion of QuCEN146 satellite drives centromere turnover in oaks by displacing ancestral LTR-rich sequences into flanking regions, with genetic drift facilitating fixation of satellite-rich centromeres. Population-scale analyses in Q. serrata reveal extensive variation in satellite rich centromeres, generated by array expansion and contraction, strand-orientation shifts, and interspecific introgression. By contrast, LTR rich centromeres of Q. variabilis exhibit extremely low polymorphism and high collinearity across populations, sustained by suppressed local recombination, linked selection, and constrained LTR dynamics. We further demonstrate chromosome-independent evolutionary patterns for both satellite-rich and LTR-rich centromeres. Collectively, these findings demonstrate how evolutionary processes drive centromere turnover and shape contrasting centromeric sequence landscapes in forest trees.
Authors
- Pamela S. Soltis (ORCID: https://orcid.org/0000-0001-9310-8659)
- Hanli You (ORCID: https://orcid.org/0000-0002-0974-8248)
- Paul S. Manos (ORCID: https://orcid.org/0000-0003-3122-1538)
- Ian R. Henderson (ORCID: https://orcid.org/0000-0001-5066-1489)
- Jeannine M. Cavender-Bares (ORCID: https://orcid.org/0000-0003-3375-9630)
- Chen Feng (ORCID: https://orcid.org/0000-0003-4971-4322)
- Yi‐Ye Liang (ORCID: https://orcid.org/0000-0002-4992-3784)
- Naili Zhang (ORCID: https://orcid.org/0000-0002-7637-9841)
- Wen-Ji Luo (ORCID: https://orcid.org/0000-0003-2868-9367)
- Rebekah Mohn (ORCID: https://orcid.org/0000-0002-7489-8939)
- Shao‐Jun Ling (ORCID: https://orcid.org/0000-0002-4675-8250)
- Keping Ma (ORCID: https://orcid.org/0000-0001-9112-5340)
- Jingshu Wang (ORCID: https://orcid.org/0000-0002-1968-6888)
- Qiongqiong Lin (ORCID: https://orcid.org/0009-0007-1344-4996)
- Biao‐Feng Zhou (ORCID: https://orcid.org/0000-0002-2782-4160)
- Yong Shi (ORCID: https://orcid.org/0000-0001-7974-1079)
- Douglas Soltis
- Pär K. Ingvarsson (ORCID: https://orcid.org/0000-0001-9225-7521)
- Audrey Tucker
- Zhao Shen
- Liang‐Jing Qiao (ORCID: https://orcid.org/0009-0006-2613-9731)
- Andrew Hipp
- Yong-Hang Run
- Wen-Li Zhang
- Yu Liang
- Baosheng Wang
- Lina Elshaer
- Jing-Wei Niu
- Zhu-Kuan Chen
- Xiao-Juan Liu
- Wei-Shu Yan
- Sheng-Chen Shan
Institutions
- Nanjing Agricultural University (CN)
- Florida Museum of Natural History (US)
- Harvard University (US)
- Duke University (US)
- Chinese Academy of Sciences (CN)
- University of Cambridge (GB)
- Morton Arboretum (US)
- Swedish University of Agricultural Sciences (SE)
- Beijing Forestry University (CN)
- University of Florida (US)
- Guangdong Academy of Agricultural Sciences (CN)
- South China Botanical Garden (CN)
- Lushan Botanical Garden (CN)
- Ministry of Agriculture and Rural Affairs (CN)
- Institute of Botany (CN)
- Yangzhou University (CN)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-11-06
- DOI
- https://doi.org/10.64898/2026.11.05.764454
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- preprint
Funders
- National Natural Science Foundation of China