Integration of single-nucleus RNA-seq, DAP-seq and bulk RNA-seq data obtained from peanut seeds

The snRNA-seq atlas resolved 13 distinct cell clusters and identified three principal seed cell types: seed coat, cotyledon and embryonic axis, further unravelling pseudotime differentiation trajectories and cell-type-specific transcriptional regulatory signatures during seed maturation.

Time-series bulk RNA-seq captured global gene expression dynamics across three key seed developmental stages (5, 25 and 45 days after peg penetration), enabling differential expression screening, weighted gene co-expression network construction, and computational deconvolution of cell-type proportions. DAP-seq was utilized to map genome-wide binding motifs and downstream target genes of AhWRI1-03a, the master transcription factor governing seed oil biosynthesis, while multi-omics data from peanut pods supplemented the spatiotemporal chromatin accessibility landscape of functional genes.