Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution

Seeds are a key lifecycle stage for many plants. Seeds are also the basis of agriculture and the primary source of calories consumed by humans (1). Here, we employ single-nucleus RNA-sequencing to generate a transcriptional atlas of developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, the primary site of gene imprinting in flowering plants, mediates the relationship between the maternal parent and embryo (2). We identify transcriptionally-uncharacterized nuclei types in the chalazal endosperm, which interfaces with maternal tissue for nutrient unloading (3,4). We demonstrate that the extent of parental bias of maternally expressed imprinted genes varies with cell cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. Thus, imprinting is spatially and temporally heterogeneous. Increased paternal expression in the chalazal region suggests that parental conflict, which is proposed to drive imprinting evolution, is fiercest at the boundary between filial and maternal tissues.