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PreprintCC BY-NCbioRxiv

Evolutionary dynamics of the pan-centromere architecture in oaks

  • Q.-Q. Lin
  • Y.-Y. Liang
  • W.-S. Yan
  • Y.-H. Run
  • H.-L. You
  • B.-F. Zhou
  • S.-J. Ling
  • Z. Shen
  • J.-S. Wang1
  • J.-W. Niu
  • W.-J. Luo
  • L.-J. Qiao
20 more authors
  • S.-C. Shan
  • L. Elshaer
  • A. Tucker
  • C. Feng
  • Y. Shi
  • R. Mohn
  • Y. Liang
  • N.-L. Zhang
  • X.-J. Liu
  • A. Hipp
  • P. S. Manos
  • J. Cavender-Bares
  • P. K. Ingvarsson
  • I. Henderson
  • D. Soltis
  • P. S. Soltis
  • K.-P. Ma
  • Z.-K. Chen
  • W.-L. Zhang
  • B. Wang1
  1. 1State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of National Forestry and Gras
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Abstract

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.

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Cite

BibTeXRIS
BibTeX
@misc{lin2026evolutionary,
  title = {{Evolutionary dynamics of the pan-centromere architecture in oaks}},
  author = {Q.-Q. Lin and Y.-Y. Liang and W.-S. Yan and Y.-H. Run and H.-L. You and B.-F. Zhou and S.-J. Ling and Z. Shen and J.-S. Wang and J.-W. Niu and W.-J. Luo and L.-J. Qiao and S.-C. Shan and L. Elshaer and A. Tucker and C. Feng and Y. Shi and R. Mohn and Y. Liang and N.-L. Zhang and X.-J. Liu and A. Hipp and P. S. Manos and J. Cavender-Bares and P. K. Ingvarsson and I. Henderson and D. Soltis and P. S. Soltis and K.-P. Ma and Z.-K. Chen and W.-L. Zhang and B. Wang},
  howpublished = {bioRxiv},
  year = {2026},
  month = nov,
  doi = {10.64898/2026.11.05.764454},
  url = {https://www.biorxiv.org/content/10.64898/2026.11.05.764454v1},
  note = {CC BY-NC},
}
RIS
TY  - UNPB
TI  - Evolutionary dynamics of the pan-centromere architecture in oaks
AU  - Q.-Q. Lin
AU  - Y.-Y. Liang
AU  - W.-S. Yan
AU  - Y.-H. Run
AU  - H.-L. You
AU  - B.-F. Zhou
AU  - S.-J. Ling
AU  - Z. Shen
AU  - J.-S. Wang
AU  - J.-W. Niu
AU  - W.-J. Luo
AU  - L.-J. Qiao
AU  - S.-C. Shan
AU  - L. Elshaer
AU  - A. Tucker
AU  - C. Feng
AU  - Y. Shi
AU  - R. Mohn
AU  - Y. Liang
AU  - N.-L. Zhang
AU  - X.-J. Liu
AU  - A. Hipp
AU  - P. S. Manos
AU  - J. Cavender-Bares
AU  - P. K. Ingvarsson
AU  - I. Henderson
AU  - D. Soltis
AU  - P. S. Soltis
AU  - K.-P. Ma
AU  - Z.-K. Chen
AU  - W.-L. Zhang
AU  - B. Wang
PY  - 2026
DA  - 2026/11/05
PB  - bioRxiv
DO  - 10.64898/2026.11.05.764454
UR  - https://www.biorxiv.org/content/10.64898/2026.11.05.764454v1
AB  - 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.
ER  -