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Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos

Author

Listed:
  • Xiaoyang Ge

    (Zhengzhou University
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

  • 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
    Institute of Cotton Research of the Chinese Academy of Agricultural Sciences)

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.

Suggested Citation

  • 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 & Men, 2025. "Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-55870-6
    DOI: 10.1038/s41467-025-55870-6
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    References listed on IDEAS

    as
    1. Alexandra Schlereth & Barbara Möller & Weilin Liu & Marika Kientz & Jacky Flipse & Eike H. Rademacher & Markus Schmid & Gerd Jürgens & Dolf Weijers, 2010. "MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor," Nature, Nature, vol. 464(7290), pages 913-916, April.
    2. Susanne C. van den Brink & Anna Alemany & Vincent van Batenburg & Naomi Moris & Marloes Blotenburg & Judith Vivié & Peter Baillie-Johnson & Jennifer Nichols & Katharina F. Sonnen & Alfonso Martinez Ar, 2020. "Publisher Correction: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids," Nature, Nature, vol. 579(7799), pages 11-11, March.
    3. Susanne C. van den Brink & Anna Alemany & Vincent van Batenburg & Naomi Moris & Marloes Blotenburg & Judith Vivié & Peter Baillie-Johnson & Jennifer Nichols & Katharina F. Sonnen & Alfonso Martinez Ar, 2020. "Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids," Nature, Nature, vol. 582(7812), pages 405-409, June.
    4. Min Cao & Rong Chen & Pan Li & Yongqiang Yu & Rui Zheng & Danfeng Ge & Wei Zheng & Xuhui Wang & Yangtao Gu & Zuzana Gelová & Jiří Friml & Heng Zhang & Renyi Liu & Jun He & Tongda Xu, 2019. "TMK1-mediated auxin signalling regulates differential growth of the apical hook," Nature, Nature, vol. 568(7751), pages 240-243, April.
    5. Tao Zhang & Sarah E. Noll & Jesus T. Peng & Amman Klair & Abigail Tripka & Nathan Stutzman & Casey Cheng & Richard N. Zare & Alexandra J. Dickinson, 2023. "Chemical imaging reveals diverse functions of tricarboxylic acid metabolites in root growth and development," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
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