Single-cell RNA sequencing(scRNA-seq)has revolutionized plant biology by enabling high-resolution analysis of cellular heterogeneity,gene expression,and regulatory networks across diverse species.Here,we present Plant...Single-cell RNA sequencing(scRNA-seq)has revolutionized plant biology by enabling high-resolution analysis of cellular heterogeneity,gene expression,and regulatory networks across diverse species.Here,we present PlantscRNAdb release 4.0,an updated comprehensive database that incorporates a new plant ontology of cell types(POCT)and covers 33 plant species.Using HCMarker,a novel computational tool developed in this study that employs a multi-metric scoring system for robust and accurate identification of marker genes across diverse plant cell types,we identified 58846 high-confidence marker genes(with 31818 assigned to POCT cell types)from 107 scRNA-seq datasets.We also provide cell-type-specific functional pathway analyses,revealing key biological roles and regulatory networks in different cell populations.In addition,we introduce PCmaster_anno,a deep-learning-based tool that harnesses the database's extensive data to improve automated plant cell-type annotation.Compared with previous releases,PlantscRNAdb release 4.0 not only adds 25 species and 52 datasets but also provides a more standardized and precise framework for interpreting plant cell types and their markers.展开更多
基金supported by Biological Breeding-Major Projects(2023 ZD04076)Yunnan Tobacco Company(2024530000241001)the China Postdoctoral Science Foundation(2023M743078).
文摘Single-cell RNA sequencing(scRNA-seq)has revolutionized plant biology by enabling high-resolution analysis of cellular heterogeneity,gene expression,and regulatory networks across diverse species.Here,we present PlantscRNAdb release 4.0,an updated comprehensive database that incorporates a new plant ontology of cell types(POCT)and covers 33 plant species.Using HCMarker,a novel computational tool developed in this study that employs a multi-metric scoring system for robust and accurate identification of marker genes across diverse plant cell types,we identified 58846 high-confidence marker genes(with 31818 assigned to POCT cell types)from 107 scRNA-seq datasets.We also provide cell-type-specific functional pathway analyses,revealing key biological roles and regulatory networks in different cell populations.In addition,we introduce PCmaster_anno,a deep-learning-based tool that harnesses the database's extensive data to improve automated plant cell-type annotation.Compared with previous releases,PlantscRNAdb release 4.0 not only adds 25 species and 52 datasets but also provides a more standardized and precise framework for interpreting plant cell types and their markers.
