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

Tran N. Chau (), Prakash Raj Timilsena, Sai Pavan Bathala, Sanchari Kundu, Bastiaan O. R. Bargmann and Song Li ()
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Tran N. Chau: Virginia Tech
Prakash Raj Timilsena: Virginia Tech
Sai Pavan Bathala: Virginia Tech
Sanchari Kundu: Virginia Tech
Bastiaan O. R. Bargmann: Virginia Tech
Song Li: Virginia Tech

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract Single-cell RNA sequencing (scRNA-seq) is widely used in plant biology and is a powerful tool for studying cell identity and differentiation. However, the scarcity of known cell-type marker genes and the divergence of marker expression patterns limit the accuracy of cell-type identification and our capacity to investigate cell-type conservation in many species. To tackle this challenge, we devise a novel computational strategy called Orthologous Marker Gene Groups (OMGs), which can identify cell types in both model and non-model plant species and allows for rapid comparison of cell types across many published single-cell maps. Our method does not require cross-species data integration, while still accurately determining inter-species cellular similarities. We validate the method by analyzing published single-cell data from species with well-annotated single-cell maps, and we show our methods can capture majority of manually annotated cell types. The robustness of our method is further demonstrated by its ability to pertinently map cell clusters from 1 million cells, 268 cell clusters across 15 diverse plant species. We reveal 14 dominant groups with substantial conservation in shared cell-type markers across monocots and dicots. To facilitate the use of this method by the broad research community, we launch a user-friendly web-based tool called the OMG browser, which simplifies the process of cell-type identification in plant datasets for biologists.

Date: 2025
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DOI: 10.1038/s41467-024-55755-0

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