Fig. 1: A transcriptional atlas of early Arabidopsis seed development.

a, Seed developmental stages profiled in this study and L1 and L2 annotations. oi2, outer integument 2; oi1, outer integument 1; ii2, inner integument 2; ii1′, inner integument 1′; ii1, inner integument 1; EMB, embryo; CPT, chalazal proliferating tissue; CZSC, chalazal seed coat; FUN, funiculus; PEN peripheral endosperm; MCE, micropylar endosperm; ESR, embryo surrounding region; CZE, chalazal endosperm; OVL, ovule. b–d, L1 (b), L2 (c) and L3 (d) annotations across all datasets. See Supplementary Table 3 for complete descriptions of all L3 annotations. e, Cell type proportions for L2 annotations in the full atlas dataset. f, Morphological stages of the embryo. g, Merged 3–7 DAP embryo datasets coloured according to annotations from f (left) and time point (right). h, Left: HCR validation of the protoderm (PDF1+), inner cotyledon (XYL4+) and vascular primordium (JUL1+) in the embryo. Scale bars, 50 µm. The PDF1 and JUL1 images are representative of signal observed in at least six seeds in two independent experiments, and the image for XYL4 represents signal observed in four seeds in one experiment. Right: expression of genes corresponding to HCR probes in the integrated embryo dataset, split by L3 annotation. y-axis labels are coloured according to tissue types in f. i, Detection of the suspensor, a rare nucleus type in the merged embryo dataset. Left: module score analysis for 29 suspensor marker genes curated in Kao et al.²⁷. Right: WOX8 is a suspensor marker gene enriched in the suspensor cluster and detected in 31 nuclei in the entire dataset. The black arrows point to the putative suspensor population.