STOmics technology:BGI Stereomics Stereo-Seq

Data type:Transcriptome or Gene expression, Spatial transcriptomics

Sample scope:Multispecies

Summary:C4 plant evolved convergently from differently lineages of C3 plants, which have higher efficiency of photosynthesis alongside higher water use efficiency and nitrogen use efficiency. Although the process of C4 photosynthesis metabolism are relatively clear, the initiation and morphogenesis of kranz anatomy is largely unclear. Although systems biology approaches have greatly advanced our understanding of C4 photosynthesis regulation, comprehensive genomic spatial transcriptomes of the C4 plant leaf are lacking, which are crucial to fully elucidate the morphogenesis mechanisms of Kranz anatomy. In this study, we utilized spatial enhanced resolution omics-sequencing (Stereo-seq) to develop a spatial transcriptomic atlas of the leaf primordium and also generated a single-nucleus transcriptomic atlas for the early stage. Combination of these spatial and snRNA-seq atlases allow us to use Semi-supervised clustering to sub-cluster and isolate a cluster of very early BSC which could not be identified by unsupervised clustering in scRNA-seq data. By integrating the spatial transcriptomes of Kranz anatomy at the same stage, we constructed a pseudo-Kranz anatomy to elucidate the diffusion expression patterns of key genes within Kranz anatomy. We found that maize SHR and SCR genes are primarily expressed in veins and MC, respectively, and are also notably overlapping in the bundle sheath cells (BSC). We constructed a conserved regulatory network for the C4 plant leaf primordium and identified key TFs that are crucial for C4 Kranz anatomy development, with a particular focus on the significantly elevated expression of SHR genes within the procambium. Among the conserved regulatory network, we validated that IDDP1 and IDD7 are implicated in controlling the morphogenesis of Kranz anatomy, potentially through their interaction with SCR genes. In summary, we established a high-throughput, high-resolution snRNA-seq and spatial transcriptomic atlas for leaf primordia across four grass species, and we have delineated a conserved gene regulatory network governing Kranz anatomy development, which serves as a valuable resource for researchers exploring grass leaf development.

Contributor(s):Zhao Caiyao, Yang Jianzhao, Chen Hanyang, Ni Anting.

Submitter:赵彩耀,BGI

Release date:2025-05-31

Updated:2024-06-24