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A single-cell multi-omics atlas of rice

Cell functions across eukaryotes are driven by specific gene expression programs, which are dependent on chromatin structure1-3. Here we report a single-cell multi-omics atlas of rice, one of the world’s major crops. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 c...

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Main Authors: Wang, Xiangyu (Author) , Huang, Huanwei (Author) , Jiang, Sanjie (Author) , Kang, Jingmin (Author) , Li, Dongwei (Author) , Wang, Kailai (Author) , Xie, Shang (Author) , Tong, Cheng (Author) , Liu, Chaofan (Author) , Hu, Guihua (Author) , Li, Haoqian (Author) , Li, Cong (Author) , Yang, Liwen (Author) , Ding, Yike (Author) , Li, Shang-Tong (Author) , Wang, Faming (Author) , Lohmann, Jan U. (Author) , Liang, Zhe (Author) , Gu, Xiaofeng (Author)
Format: Article (Journal)
Language:English
Published: 09 July 2025
In: Nature
Year: 2025, Volume: 644, Issue: 8077, Pages: 722-730, [1-23]
ISSN:1476-4687
DOI:10.1038/s41586-025-09251-0
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1038/s41586-025-09251-0
Verlag, lizenzpflichtig, Volltext: https://www.nature.com/articles/s41586-025-09251-0
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Author Notes:Xiangyu Wang, Huanwei Huang, Sanjie Jiang, Jingmin Kang, Dongwei Li, Kailai Wang, Shang Xie, Cheng Tong, Chaofan Liu, Guihua Hu, Haoqian Li, Cong Li, Liwen Yang, Yike Ding, Shang-Tong Li, Faming Wang, Jan U. Lohmann, Zhe Liang & Xiaofeng Gu
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Summary:Cell functions across eukaryotes are driven by specific gene expression programs, which are dependent on chromatin structure1-3. Here we report a single-cell multi-omics atlas of rice, one of the world’s major crops. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs, we identified cell-type-specific gene regulatory networks and described novel cell states, such as a ‘transitional state’ in floral meristems. On the basis of our network analyses, we uncovered the function of the cell-type-specific regulatory hubs RSR1, F3H and LTPL120 during rice development. Our analysis revealed correlations between cell type and agronomic traits, as well as conserved and divergent cell-type functions during evolution. In summary, this study not only offers a unique single-cell multi-omics resource for a major crop but also advances our understanding of cell-type functions and the underlying molecular programs in rice.
Item Description:Gesehen am 25.11.2025
Physical Description:Online Resource
ISSN:1476-4687
DOI:10.1038/s41586-025-09251-0

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