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PlantscRNAdb 4.0: Improved marker identification and annotation under a cell-type uniformity for plants
Dihuai Zheng1, Xiaolin Lu1, Yaqian Lu2
1Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
Molecular Plant
|December 26, 2025
Summary
PlantscRNAdb Release 4.0 enhances plant cell type analysis with a new ontology and 58,846 marker genes identified using the novel HCMarker tool. This updated database improves cell type annotation and functional pathway insights across 33 plant species.
Area of Science:
- Plant Biology
- Genomics
- Bioinformatics
Background:
- Single-cell RNA sequencing (scRNA-seq) offers high-resolution insights into plant cellular heterogeneity and gene expression.
- Existing databases may lack comprehensive cell type ontologies and marker gene annotations across diverse plant species.
Purpose of the Study:
- To present PlantscRNAdb Release 4.0, an updated database featuring a new plant ontology of cell types (POCT).
- To identify high-confidence marker genes and perform cell type-specific functional analyses.
- To introduce novel computational tools for marker gene identification and cell type annotation.
Main Methods:
- Development and application of HCMarker, a computational tool for identifying marker genes using a multi-metric scoring system.
- Integration of 107 scRNA-seq datasets covering 33 plant species.
- Development of PCmaster_anno, a deep learning tool for automated plant cell type annotation.
Main Results:
- Identification of 58,846 high-confidence marker genes, with 31,818 assigned to POCT cell types.
- Cell type-specific functional pathway analyses revealing key biological roles and regulatory networks.
- Release 4.0 includes 25 new species and 52 new datasets compared to previous versions.
Conclusions:
- PlantscRNAdb Release 4.0 provides a standardized and precise framework for interpreting plant cell types and their markers.
- The database and associated tools (HCMarker, PCmaster_anno) advance plant single-cell genomics research.
- This resource facilitates deeper understanding of cellular diversity and function in plants.
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