A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of fertilization, and the maternal seed coat. Understanding of transcriptional programs that underlie tissue-specific functions and coordination in Arabidopsis seeds is incomplete. To address this, we performed single nucleus RNA-sequencing on seeds at 3, 5, and 7 days after pollination. We characterize all major seed cell types, further refine transcriptional states in the endosperm, and report previously transcriptionally undefined cell types in the seed coat. Among other findings, our analyses reveal the compartmentalization of genes involved in brassinsteroid-responsive transcription factor activation and nutrient transport. Additionally, we identify abundant cell-type specific expression of genes that encode rapidly evolving short, secreted peptides (SSPs) in the micropylar and chalazal endosperm, suggesting that SSP activity is an unexplored but potentially significant contributor to Arabidopsis seed development. Two biological replicates, (different plants hand pollinated and processed for snRNA-seq on different days) each containing seeds dissected from 10-15 Arabidopsis thaliana col-0 siliques (500-800 seeds), were collected for each timepoint (3, 5, and 7 days after pollination), producing six replicates total. Each biological replicate was processed individually using one Chromium Next GEM Single Cell 3’ Kit (v3.1) reaction with a target nuclei recovery of 10k, except for one 3DAP biological replicate, which was split across two reactions. In total, 7 libraries were generated in this study.