Objective This study aimed to explore the application of cross-species single-cell integration methods in plants to uncover the transcriptional conservation and divergence of shoot apical meristem (SAM) cell types between Phyllostachys edulis (moso bamboo) and Arabidopsis thaliana.

Method Based on identified orthologous gene pairs, we integrated single-cell transcriptomic data from the SAM of moso bamboo and arabidopsis, using canonical correlation analysis (CCA) for batch correction to eliminate species-specific technical biases. Uniform manifold approximation and projection (UMAP) was applied to visualize the distribution patterns of integrated cells. Furthermore, Spearman correlation analysis and identification of cross-species marker genes were performed to assess transcriptional similarity and functional characteristics of different cell types.

Result (1) A total of 23 cell clusters were identified. In the UMAP space, most cells clustered separately based on their species origin, but some cell clusters showed significant overlap, suggesting high transcriptomic similarity. (2) Further analysis revealed that the overlapping region mainly consisted of epidermal and vascular tissue cells, indicating the evolutionary conservation of these tissues. Correlation analysis further supported the high similarity in gene expression patterns among conserved cell types, while other cell clusters exhibited greater species specificity and consisted of mixed cell types. (3) 183 cross-species conserved marker genes were identified. These genes were specifically expressed in corresponding cell types of both species. Functional analysis revealed their key roles in plant development and evolution.

Conclusion This study revealed the core functional characteristics of conserved cell types between moso bamboo and arabidopsis, providing new perspectives on plant evolutionary mechanisms and laying a data foundation for functional gene discovery and research in non-model plants.