A cis-regulatory atlas of rice single cells

Cis-regulatory elements (CREs) are essential in precisely regulating gene expression, contributing significantly to the evolution of species. Identifying cell-type-specific CREs is essential for understanding plant evolution, domestication, and improving crops through genome editing. Here, we built a cis-regulatory atlas in Oryza sativa, encompassing 106,143 nuclei representing 138 discrete cell states from nine distinct organs. Within syntenic regions shared with four other grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, and Urochloa fusca), we identified 10,219 cell-type-specific accessible chromatin regions (ACRs), serving as sources for investigating divergence of these species. To elucidate the roles of cell-type-specific ACRs in species divergence, we focused on leaf cells in O. sativa and the aforementioned grass species. We observed species-specific candidate CREs (cCREs) potentially associated with cell differentiation, especially in epidermal cells across species. These data also revealed presence of H3K27me3-associated ACRs in the majority of cell types across different organs and species, potentially harboring silencer cCREs. Together, this study significantly advances our understanding of the role of cCREs during cell differentiation, shedding light on their contribution to species divergence in plants All samples were integrated into a single all vs. all analysis. Several organs (axillary buds, seedlings, seminal roots, crown roots, panicles, seeds, etc) were profiled with biological replicates.