Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes

Area of Science:

• Plant biology
• Genomics
• Computational biology

Background:

• Single-cell RNA sequencing (scRNA-seq) is crucial for plant cell identity studies.
• Limited known marker genes and divergent expression hinder accurate cell-type identification and cross-species comparisons.

Purpose of the Study:

• To develop a computational method for accurate plant cell-type identification across species.
• To enable rapid comparison of cell types using single-cell data from model and non-model plants.
• To identify conserved cell-type markers across diverse plant species.

Main Methods:

• Developed Orthologous Marker Gene Groups (OMGs), a novel computational strategy.
• OMGs does not require cross-species data integration for inter-species similarity determination.
• Validated OMGs on published scRNA-seq data from multiple plant species, including large-scale datasets.

Main Results:

• OMGs accurately captures the majority of manually annotated cell types.
• The method robustly maps cell clusters from over 1 million cells across 15 plant species.
• Identified 14 dominant conserved cell-type marker groups across monocots and dicots.

Conclusions:

• OMGs provides a robust and scalable approach for plant cell-type identification and cross-species comparison.
• The method overcomes limitations of marker gene scarcity and expression divergence.
• A user-friendly web tool, the OMG browser, is launched to facilitate broader research application.