Homology and ontogeny of the grass cotyledon: A multiplexed transcriptomic analysis

The goal of the project is to investigate the transcriptomic relationship between maize embryo lateral organs, scutellum, coleoptile and foliar leaf, and to study the homology and ontogeny of the grass cotyledon. To achieve this goal, we profiled the single-cell transcriptomic landscape of the Leaf1 maize embryo, the earliest timepoint when all these lateral organs are formed. In addition, we performed Laser Microdissection RNA-seq (LM RNA-seq) and spatial transcriptomic (ST) analyses to annotate the spatial information on single-cell clusters. Also, conventional and multiplex in situ hybridization analyses were conducted in the transition, coleoptilar and the Leaf1 stage embryo to verify single cell cluster identity as well as to investigate the gene expression pattern of the lateral organ initiation.