RNA sequencing of developing Mimulus seeds reveals conservation of three imprinted genes

The seeds of angiosperms are comprised of three main tissues--the seed coat, embryo, and endosperm--whose coordinated development will enable the next generation to disperse with sufficient maternal resources and germinate when conditions are favorable. We use high-throughput RNA sequencing technology to characterize the developmental dynamics of gene expression in whole seeds resulting from a compatible cross between two species of the Mimulus guttatus complex.We find that development in ovules and seeds involves the activation of the majority of annotated genes in M. guttatus (64-67%), and the differential expression over time of 6,691 genes, including 424 transcription factors. Most of the genes we detected (69%) were expressed at all stages, from ovules to heart-stage embryo seeds. We also detected and validated four genes exhibiting paternally-biased expression (MDB13, ATXR5, DnaJ and BGAL11). Intriguingly, three of our validated PEGs are have imprinted homologues in other plant species, suggesting that these proteins perform a shared role in endosperm development among distantly related plant taxa. Additionally, the overlap in gene expression profiles between stages of development suggests that most genes fulfill multiple developmental and biological roles. Future analyses should examine whether different regions of the seed (embryo, endosperm, and seed coat) have unique patterns of gene expression, and the extent to which spatial coordination and regulation of gene expression may play a role in regulating seed development. Inbred lines of Mimulus guttatus (CSS4) and the selfing species Mimulus pardalis (SEC39) were grown in a chamber at 18-hour days, 21°C, 30% relative humidity.Total RNA was extracted from ovules and developing hybrid seeds from that had been removed from longitudinal-sectioned fruits. We sequenced a total of 20 samples, including 5 replicates of un-pollinated M. pardalis ovules and 3-5 replicates of M. pardalis x M. guttatus hybrid seeds collected at 2, 4, 6, and 8 DAP. Each replicate contained ~10-20 ovaries or fruits pooled from different plants.