A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat
The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.
Authors
- Xing Wang Deng (ORCID: https://orcid.org/0000-0001-8709-1467)
- Yunbi Xu (ORCID: https://orcid.org/0000-0003-3361-4650)
- Xiuru Dai (ORCID: https://orcid.org/0000-0002-2516-1068)
- Hang He (ORCID: https://orcid.org/0000-0003-3165-283X)
- Guochen Qin (ORCID: https://orcid.org/0000-0002-2048-8571)
- Jianxin Bian (ORCID: https://orcid.org/0000-0001-6443-7218)
- Yongqi Liu (ORCID: https://orcid.org/0000-0003-2090-0017)
- Zhaoxu Gao (ORCID: https://orcid.org/0000-0002-5398-8054)
- Shoucheng Liu (ORCID: https://orcid.org/0000-0002-0138-0995)
- Da Ren (ORCID: https://orcid.org/0009-0009-7287-4501)
- Bosheng Li (ORCID: https://orcid.org/0000-0002-1816-7007)
- Bao‐Hua Song (ORCID: https://orcid.org/0000-0003-3537-7783)
- Yang Chen (ORCID: https://orcid.org/0000-0002-1811-8483)
- Xiaofeng Chen (ORCID: https://orcid.org/0000-0001-6577-5681)
- Xiaopeng Li (ORCID: https://orcid.org/0000-0001-7926-193X)
- Kui Li (ORCID: https://orcid.org/0000-0002-3942-3911)
- Jian Li (ORCID: https://orcid.org/0000-0003-3007-1443)
- Dongdong Lu (ORCID: https://orcid.org/0000-0001-5163-0115)
- Weimin Liu (ORCID: https://orcid.org/0000-0001-7843-5766)
- Shisheng Chen (ORCID: https://orcid.org/0000-0002-8617-4356)
- Xiaoqin Liu (ORCID: https://orcid.org/0000-0001-9232-3461)
Institutions
- Center for Life Sciences (CN)
- Weifang University (CN)
- Shandong Agricultural University (CN)
Publication Details
- Journal
- Nature Genetics
- Published
- 2025-04-01
- DOI
- https://doi.org/10.1038/s41588-025-02137-x
- Citations
- 38
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 66.49