Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development
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...
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-55869-z |
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| author | 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 Xiongfeng Ma |
| author_facet | 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 Xiongfeng Ma |
| author_sort | Xuwu Sun |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-36463e0cdf154d0aaa2bc014d1094e01 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-36463e0cdf154d0aaa2bc014d1094e012025-08-20T03:05:52ZengNature PortfolioNature Communications2041-17232025-01-0116112110.1038/s41467-025-55869-zSpatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early developmentXuwu Sun0Aizhi Qin1Xingxing Wang2Xiaoyang Ge3Zhixin Liu4Chenxi Guo5Xiaole Yu6Xianliang Zhang7Yao Lu8Jincheng Yang9Jiuming He10Yaping Zhou11Yumeng Liu12Mengke Hu13Hao Liu14Zihao Zhao15Guanjing Hu16Wei Li17Xinshan Zang18Shuai Dai19Susu Sun20Lenin Yong-Villalobos21Luis Herrera-Estrella22Lam-Son Phan Tran23Xiongfeng Ma24State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesShanghai OE Biotech Co., LtdState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical CollegeState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan UniversityInstitute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech UniversityInstitute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech UniversityInstitute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech UniversityState Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of the Chinese Academy of Agricultural SciencesAbstract 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.https://doi.org/10.1038/s41467-025-55869-z |
| spellingShingle | 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 Xiongfeng Ma Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development Nature Communications |
| title | Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development |
| title_full | Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development |
| title_fullStr | Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development |
| title_full_unstemmed | Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development |
| title_short | Spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development |
| title_sort | spatiotemporal transcriptome and metabolome landscapes of cotton fiber during initiation and early development |
| url | https://doi.org/10.1038/s41467-025-55869-z |
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