Structural composition and evolution of jujube centromere reveal a dominant role for LTR retrotransposon

Abstract

Centromeres are essential for centromere-specific histone H3 (CENH3) recruitment and kinetochore assembly, ensuring accurate chromosome segregation and maintaining genome stability in plants. Although extensively studied in model species, the structural organization of centromeres in nonmodel plants, such as fruit trees, remains poorly explored. Our previous study revealed that jujube centromeres lack the typical tandem repeat (TR)-rich structure, complicating their precise identification. In this study, we updated the genome assembly of jujube (Ziziphus jujuba Mill. ‘Dongzao’) to a haplotype-resolved T2T version, enabling accurate mapping and comparison of centromeres between haplotypes using CENH3 ChIP-seq. These centromeres, ranging from 0.75 to 1.40 Mb, are largely conserved between haplotypes, except for a localized inversion on chromosome 10. Unlike the TR-rich centromeres found in many plant species, jujube centromeres are predominantly composed of Gypsy-type long-terminal repeat retrotransposons (LTR-RTs). Among these, we identified a centromere-enriched LTR family, centromeric retrotransposons of jujube (CRJ), which is particularly abundant in terminal LTRs compared to the internal transposon regions. Comparative analysis across plant species revealed that centromeric retrotransposons primarily fall into three subfamilies—CRM, Tekay, and Athila—highlighting strong subfamily specificity. Notably, early insertions of CRJ-derived LTR segments contributed to the formation of TR-like structures, suggesting a mechanistic link between transposable elements and the evolution of centromeric tandem repeats. This work provides the first in-depth characterization of a TE-dominated centromere architecture in a fruit tree, offering new insights into the diversity and evolution of plant centromeres.

Acknowledgments

We thank Dr. Wei Huang (College of Agronomy and Biotechnology, China Agricultural University) for providing technical support in the FISH experiments. This work was supported by the National Natural Science Foundation of China (grant no. 32171817), the Natural Science Foundation of Hebei Province (grant no. C2022204030), and the Special Research Project for New Talent of Hebei Agricultural University (grant no. YJ2020025).

Author contributions

M.Y. conceived the project; D.L., Y.L., J.G., J.S., G.L., and Z.L. prepared samples and performed the experiments; D.L., M.Y, Z.Z., S.Z., Y.Y., J.L., and G.W. performed the data analysis; D.L. and M.Y. draft the manuscript; M.Y. revised the manuscript; M.L. supervised the work. All authors have reviewed and approved the manuscript.

Data availability

The raw data of ChIP-seq are deposited in the National Genomics Data Center with BioProject: PRJCA039671. The haplotype-resolved genome and annotation file have been shared in the figshare repository at https://figshare.com/s/e040dc92e6ceb9ec232d.

Conflict of interest statement

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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