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<p>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., <i>DOX2</i>, <i>KCS19.4</i>, <i>BEE3</i>, and <i>HOS3.7</i>) 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 <i>GhBEE3</i>/<i>Gh_A09G062900</i> in cotton fiber initiation. We also construct a publicly accessible website (<a href="https://cotton.cricaas.com.cn/ovule/">https://cotton.cricaas.com.cn/ovule/</a>) for visualization of the spatiotemporal gene expression in cotton, providing a reference dataset for further studies on cotton fiber development.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年1月20日

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  • 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

摘要

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.