Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos

Xiaoyang Ge, Xiaole Yu, Zhixin Liu, Jiachen Yuan, Aizhi Qin, Ye Wang, Yanli Chen, Wenqiang Qin, Yumeng Liu, Xingxing Liu, Yaping Zhou, Peng Wang, Jincheng Yang, Hao Liu, Zihao Zhao, Mengke Hu, Yixin Zhang, Susu Sun, Luis Herrera-Estrella, Lam-Son Phan Tran, Xuwu Sun () and Fuguang Li ()
Additional contact information
Xiaoyang Ge: Zhengzhou University
Xiaole Yu: Henan University
Zhixin Liu: Henan University
Jiachen Yuan: Zhengzhou University
Aizhi Qin: Henan University
Ye Wang: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Yanli Chen: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Wenqiang Qin: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Yumeng Liu: Henan University
Xingxing Liu: Zhengzhou University
Yaping Zhou: Henan University
Peng Wang: Institute of Cotton Research of the Chinese Academy of Agricultural Sciences
Jincheng Yang: Henan University
Hao Liu: Henan University
Zihao Zhao: Henan University
Mengke Hu: Henan University
Yixin Zhang: Henan University
Susu Sun: Henan University
Luis Herrera-Estrella: Texas Tech University
Lam-Son Phan Tran: Texas Tech University
Xuwu Sun: Henan University
Fuguang Li: Zhengzhou University

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

Abstract: Abstract Somatic embryogenesis (SE) is a developmental process related to the regeneration of tissue-cultured plants, which serves as a useful technique for crop breeding and improvement. However, SE in cotton is difficult and elusive due to the lack of precise cellular level information on the reprogramming of gene expression patterns involved in somatic embryogenesis. Here, we investigate the spatial and single-cell expression profiles of key genes and the metabolic patterns of key metabolites by integrated single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics (ST), and spatial metabolomics (SM). To evaluate the results of these analyses, we functionally characterized the potential roles of two representative marker genes, AATP1 and DOX2, in the regulation of cotton somatic embryo development. A publicly available web-based resource database ( https://cotton.cricaas.com.cn/somaticembryo/ ) in this study provides convenience for future studies of the expression patterns of marker genes at specific developmental stages during the process of SE in cotton.

Date: 2025
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DOI: 10.1038/s41467-025-55870-6

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