scPlantReg: A Comprehensive platform for single-cell chromatin accessibility and cis-regulatory analysis in plants

Gene regulation is highly cell-type-specific, yet plant-specific single-cell ATAC-seq (scATAC-seq) frameworks and cross-species databases to study it remain limited. Here, we present scPlantReg, an integrated framework and database for plant scATAC-seq data. The platform enables end-to-end analysis from raw data processing to biological interpretation and includes a new supervised machine learning approach for accurate cell-type annotation. Using scPlantReg framework, we constructed the first single-cell chromatin landscape of pearl millet, revealing WRKY transcription factors as key regulators of xylem development. We further applied the framework to re-analyze scATAC-seq datasets from eight plant species, spanning 11 tissues and multiple developmental stages, and integrated these data into the scPlantReg database to enable cross-species comparisons. We identified evolutionarily conserved cis-regulatory elements, including MYB96 motifs in epidermal cells, KUA1 in mesophyll cells, and ATHB-6 in phloem companion cells. By combining the framework with standardized datasets, scPlantReg serves as a comprehensive resource for uncovering cellular gene regulatory mechanisms and advancing plant improvement.