Fig. 1: Identifying cell types and characterizing ACRs in rice using scATAC-seq data.

a, Overview of cell types in leaf, root, seed and panicle organs. SBM, secondary branch meristem; PBM, primary branch meristem; SM, spikelet meristem; FM, floral meristem. b, UMAP projection of nuclei, distinguished by assigned cell-type labels in axillary bud, early seedling (7 days after sowing), seedling (14 days after sowing), leaf (V4 stage; four leaves with visible leaf collars), seminal root, crown root, panicle, early seed development (6 DAP) and late seed development (10 DAP). SAM, shoot apical meristem; VAS cells, vasculature-related cells; *VAS cells, vasculature-related cells that were further distinguished as procambial meristem, developing phloem/xylem, developing phloem/xylem precursor, vascular parenchyma/sclerenchyma, xylem parenchyma, and companion cell and sieve elements in Supplementary Fig. 6; CC and SE, companion cell and sieve elements; CSE, central starchy endosperm; DSE, dorsal starchy endosperm; LSE, lateral starchy endosperm; SVB, scutellar vascular bundle. c, A screenshot illustrates the examples of cell-type-specific and broad ACRs. d, Evaluation of proportions of ACRs that are cell-type specific versus broad. e, ACRs show a bimodal distribution of distance to the nearest gene. The ACRs were categorized into three major groups based on their locations to the nearest gene: genic ACRs (overlapping a gene), proximal ACRs (located within 2 kb of genes) and distal ACRs (situated more than 2 kb away from genes).