PscOA: a plant scRNA-seq marker gene database for enhanced cellular transcriptome understanding

Single-cell RNA sequencing (scRNA-seq) enables high-resolution transcriptome analysis, enabling the study of cellular heterogeneity beyond bulk transcriptomics. However, plant science lags behind animal science in this field largely due to limited marker genes. In this study, we developed Plant single-cell Original Analyses (PscOA) (http://sdau.biodb.com.cn/pscoa/), a plant scRNA-seq marker gene database with 39 347 marker genes. PscOA integrates Basic Local Alignment Search Tool (BLAST) for homology-based marker gene mining, and A Cell Type Annotation Tool for Single-Cell RNA-seq Data (SCSA) for cell type annotation, complemented by visualization tools. Case studies in Arabidopsis thaliana and Populus alba L. demonstrate the potential of cell type annotation in PscOA. Leveraging A. thaliana marker genes from PscOA, we predict 258 potential markers in Nicotiana tabacum, showcasing its marker gene discovery potential for specific species. Differential expression analysis under stress reveals common and diverse strategies at the single-cell level, offering insights into plant cell type diversity and function. Altogether, PscOA serves as a valuable repository for original scRNA-seq analysis in plant science, deepening our understanding of the plant cellular transcriptome.