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Post-polyploidization centromere evolution in cotton

Nature Genetics volume 57, pages 1021–1030 (2025)Cite this article

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Abstract

Upland cotton (Gossypium hirsutum) accounts for more than 90% of the world’s cotton production and, as an allotetraploid, is a model plant for polyploid crop domestication. In the present study, we reported a complete telomere-to-telomere (T2T) genome assembly of Upland cotton accession Texas Marker-1 (T2T-TM-1), which has a total size of 2,299.6 Mb, and annotated 79,642 genes. Based on T2T-TM-1, interspecific centromere divergence was detected between the A- and D-subgenomes and their corresponding diploid progenitors. Centromere-associated repetitive sequences (CRCs) were found to be enriched for Gypsy-like retroelements. Centromere size expansion, repositioning and structure variations occurred post-polyploidization. It is interesting that CRC homologs were transferred from the diploid D-genome progenitor to the D-subgenome, invaded the A-subgenome and then underwent post-tetraploidization proliferation. This suggests an evolutionary advantage for the CRCs of the D-genome progenitor, presents a D-genome-adopted inheritance of centromere repeats after polyploidization and shapes the dynamic centromeric landscape during polyploidization in polyploid species.

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Fig. 1: T2T assembly of the TM-1 genome.
Fig. 2: Identification of the centromeres in tetraploid (TM-1) cotton.
Fig. 3: Characterization of the Gh149 repeat sequence.
Fig. 4: Comparison between diploid genomes and their corresponding subgenomes of the tetraploid.
Fig. 5: A model of cotton centromere evolution.

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Data availability

The T2T-TM-1 assembly is available at the GenBank (accession no. JBJYSO000000000) and NCBI (accession no. PRJNA1197584). The assembly and annotation are also available at http://cotton.zju.edu.cn and the figshare database website (https://figshare.com/s/e7448929553e1073acaa). The genome-sequencing data used for TM-1-T2T assembly, including PacBio HiFi data and ultralong ONT data, were deposited in the NCBI database (accession nos. PRJNA1161022 and PRJNA1196658) and China National Genomics Data (https://ngdc.cncb.ac.cn) (accession no. PRJCA021201). The raw transcriptomics data used for annotation were deposited in the NCBI database (accession no. PRJNA1162026) and China National Genomics Data (accession no. PRJCA021339). The ChIP–seq data used for centromere identification were deposited in the NCBI database (accession no. PRJNA1162014) and China National Genomics Data (accession no. PRJCA021342).

Code availability

The codes used in the present study are available via Zenodo at https://doi.org/10.5281/zenodo.13294045 (ref. 100).

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Acknowledgements

The present study was financially supported by grants from the National Key R&D Program of China (grant no. 2022YFF1001400 to L.F.), the Fundamental Research Funds for the Central Universities (grant no. 226-2022-00100 to T.Z.), the National Natural Science Foundation of China (grant nos. 32130075 to T.Z. and 32070544 to K.W.), Xinjiang Production and Construction Corps (grant no. 2023AA008 to T.Z.) and postdoctoral innovative talents support program (grant no. 517000-X92308 to S.J.). We thank Y. X. Zhu (Wuhan University), Z. J. Chen (University of Texas at Austin), S. X. Yu (Institute of Cotton Research of the Chinese Academy of Agricultural Sciences), F. G. Li (Institute of Cotton Research of the Chinese Academy of Agricultural Sciences), Z. Y. Ma (Hebei Agricultural University), X. L. Zhang (Huazhong Agricultural University), J. A. Udall (Crop Germplasm Research Unit) and J. F. Wendel (Iowa State University), who kindly released cotton genomes for comparisons in this Article.

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  1. These authors contributed equally: Hu Yan, Jinlei Han, Shangkun Jin.

Authors and Affiliations

  1. Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Key Laboratory of Plant Factory Generation-adding Breeding, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China

    Hu Yan, Shangkun Jin, Zegang Han, Zhanfeng Si, Sunyi Yan, Lisha Xuan, Xueying Guan, Lei Fang & Tianzhen Zhang

  2. School of Life Sciences, Nantong University, Nantong, China

    Jinlei Han, Guangrun Yu & Kai Wang

  3. Hainan Institute of Zhejiang University, Sanya, China

    Xueying Guan, Lei Fang & Tianzhen Zhang

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Contributions

T.Z. conceived the research project and designed the experiments. Y.H., S.Y., L.X., X.G. and L.F. assembled the TM-1-T2T genome; K.W., J.H. and G.Y. conducted molecular cytogenetic and centromeric analysis. J.H., S.J., Z.H., Z.S. X.G. and L.F. analyzed the bioinformatic data. T.Z., Y.H., S.J., J.H. and K.W. participated in writing and revising the paper. All authors discussed the results and commented on the paper.

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Correspondence to Lei Fang, Kai Wang or Tianzhen Zhang.

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Yan, H., Han, J., Jin, S. et al. Post-polyploidization centromere evolution in cotton. Nat Genet 57, 1021–1030 (2025). https://doi.org/10.1038/s41588-025-02115-3

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