Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity

The different steps of alternative splicing (AS) in plants and its regulatory mechanisms have already been studied extensively. Its broader impact on cell identity, plant immunity-related genes, and their study as a whole remains to be investigated. Using transgenic plants, we sorted 11 different Arabidopsis thaliana cell types ranging from root to aerial organs using fluorescence-activated cell sorting. RNA-seq data were analyzed with vast-tools and enabled us to generate a high-resolution AS landscape across multiple cell types, all collected through the same experimental procedure. The analysis of cell type-specific gene expression and alternative splicing events highlights the importance of AS on transcription and AS regulation itself. AS is also shown to be tightly linked to cell identity. By using closely related cell types, we captured alternative splicing events involved in specific stages of plant development. The columella cells, among others, show intensified AS regulation and an interesting splicing profile, especially regarding immunity-related genes. Overall, our analysis brings a valuable tool in the study of cell type identity, plant immunity, and AS.