Cross-species single-cell annotation with orthologous marker gene groups

Abstract

Single-cell RNA sequencing (scRNA-seq) technology has been widely used in characterizing various cell types from in plant growth and development1-6. Applications of this technology in Arabidopsis have benefited from the extensive knowledge of cell-type identity markers7,8. Contrastingly, accurate labeling of cell types in other plant species remains a challenge due to the scarcity of known marker genes9. Various approaches have been explored to address this issue; however, studies have found many closest orthologs of cell-type identity marker genes in Arabidopsis do not exhibit the same cell-type identity across diverse plant species10,11. To address this challenge, we have developed a novel computational strategy called Orthologous Marker Gene Groups (OMGs). We demonstrated that using OMGs as a unit to determine cell type identity enables assignment of cell types by comparing 15 distantly related species. Our analysis revealed 14 dominant clusters with substantial conservation in shared cell-type markers across monocots and dicots.