Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development

Xuwu Sun, Aizhi Qin, Xingxing Wang, Xiaoyang Ge, Zhixin Liu, Chenxi Guo, Xiaole Yu, Xianliang Zhang, Yao Lu, Jincheng Yang, Jiuming He, Yaping Zhou, Yumeng Liu, Mengke Hu, Hao Liu, Zihao Zhao, Guanjing Hu, Wei Li, Xinshan Zang, Shuai Dai, Susu Sun, Lenin Yong-Villalobos, Luis Herrera-Estrella, Lam-Son Phan Tran and Xiongfeng Ma ()
Additional contact information
Xuwu Sun: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Aizhi Qin: Henan University
Xingxing Wang: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Xiaoyang Ge: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Zhixin Liu: Henan University
Chenxi Guo: Henan University
Xiaole Yu: Henan University
Xianliang Zhang: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Yao Lu: Ltd
Jincheng Yang: Henan University
Jiuming He: Chinese Academy of Medical Sciences and Peking Union Medical College
Yaping Zhou: Henan University
Yumeng Liu: Henan University
Mengke Hu: Henan University
Hao Liu: Henan University
Zihao Zhao: Henan University
Guanjing Hu: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Wei Li: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Xinshan Zang: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Shuai Dai: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Susu Sun: Henan University
Lenin Yong-Villalobos: Texas Tech University
Luis Herrera-Estrella: Texas Tech University
Lam-Son Phan Tran: Texas Tech University
Xiongfeng Ma: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-21

Abstract: Abstract Cotton fibers are single cells that develop from the epidermal cells in the outer integument of developing seeds. The processes regulating fiber cell development have been extensively studied; however, the spatiotemporal transcriptome and metabolome profiles during the early stages of fiber development remain largely unknown. In this study, we profile the dynamics of transcriptome and metabolome during the early stages of cotton fiber cell development using a combination of spatial transcriptomic, single-cell transcriptomic, and spatial metabolomic analyses. We identify the key genes (e.g., DOX2, KCS19.4, BEE3, and HOS3.7) and metabolites (e.g., linoleic acid, spermine, spermidine, and α-linolenic acid) that may regulate the early development of fiber cells. Finally, knockdown and gain-of-function analyses identify the crucial role of GhBEE3/Gh_A09G062900 in cotton fiber initiation. We also construct a publicly accessible website ( https://cotton.cricaas.com.cn/ovule/ ) for visualization of the spatiotemporal gene expression in cotton, providing a reference dataset for further studies on cotton fiber development.

Date: 2025
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DOI: 10.1038/s41467-025-55869-z

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