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Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination.
Yao, Jie; Chu, Qinjie; Guo, Xing; Shao, Wenwen; Shang, Nianmin; Luo, Kang; Li, Xiaohan; Chen, Hongyu; Cheng, Qing; Mo, Fangyu; Zheng, Dihuai; Xu, Fan; Guo, Fu; Zhu, Qian-Hao; Deng, Shuiguang; Chu, Chengcai; Xu, Xun; Liu, Huan; Fan, Longjiang.
Afiliación
  • Yao J; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China.
  • Chu Q; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
  • Guo X; BGI Research, Shenzhen 518103, China; BGI Research, Wuhan 430074, China.
  • Shao W; BGI Research, Shenzhen 518103, China; BGI Research, Wuhan 430074, China.
  • Shang N; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
  • Luo K; College of Computer Science and Technology & Polytechnic Institute, Zhejiang University, Hangzhou 310015, Zhejiang, China.
  • Li X; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
  • Chen H; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
  • Cheng Q; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
  • Mo F; Hainan Institute, Zhejiang University, Sanya 572025, China.
  • Zheng D; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
  • Xu F; College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
  • Guo F; Hainan Institute, Zhejiang University, Sanya 572025, China.
  • Zhu QH; CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia.
  • Deng S; College of Computer Science and Technology & Polytechnic Institute, Zhejiang University, Hangzhou 310015, Zhejiang, China.
  • Chu C; Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
  • Xu X; BGI Research, Shenzhen 518103, China.
  • Liu H; BGI Research, Shenzhen 518103, China. Electronic address: liuhuan@genomics.cn.
  • Fan L; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Sanya 572025, China. Electronic address: fanlj@zju.edu.cn.
Dev Cell ; 59(17): 2320-2332.e5, 2024 Sep 09.
Article en En | MEDLINE | ID: mdl-38848718
ABSTRACT
Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oryza / Semillas / Germinación / Regulación de la Expresión Génica de las Plantas / Transcriptoma Idioma: En Revista: Dev Cell Asunto de la revista: EMBRIOLOGIA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oryza / Semillas / Germinación / Regulación de la Expresión Génica de las Plantas / Transcriptoma Idioma: En Revista: Dev Cell Asunto de la revista: EMBRIOLOGIA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos