PscOA: A Plant scRNA-seq Marker Gene Database for Enhanced Cellular Transcriptome Understanding

Plant Cell Physiol. 2025 Nov 17:pcaf151. doi: 10.1093/pcp/pcaf151. Online ahead of print.

ABSTRACT

Single-cell RNA sequencing (scRNA-seq) enables high-resolution transcriptome analysis, enabling the study of cellular heterogeneity beyond bulk transcriptomics. However, plant science lags animal science in the field largely due to limited sssssssssmarker genes. This study developed PscOA (http://sdau.biodb.com.cn/pscoa/), a plant scRNA-seq marker gene database with 39 347 marker genes. PscOA integrates BLAST for homology-based marker gene mining, and SCSA for cell type annotation, complemented by visualization tools. Case studies in A. thaliana and P. alba 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 the understanding of plant cellular transcriptome.

PMID:41247320 | DOI:10.1093/pcp/pcaf151