Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration

作者：Huihui� Guo, Li Xia Zhang, Haixia Guo, Xiwang Cui, Yupeng Fan, Tongtong Li, Xiushan Qi, Tongdi Yan, Anchen Chen, Fengjuan Shi, Fanchang Zeng · 发表于：PLANT PHYSIOLOGY · 年份：2024 · DOI：10.1093/plphys/kiae107 · 被引用次数：18 · 研究领域：Single-cell and spatial transcriptomics、CRISPR and Genetic Engineering、Molecular Biology Techniques and Applications

Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into four broad populations with six distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differe...