High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs) contribute to the specialized functions of cells within an organ is poorly understood. We generated a comprehensive dataset of gene expression from individual cell types of the Arabidopsis root. Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. Cell-type-specific intron retention suggested a possible origin for this common form of alternative splicing. Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with this hypothesis, distinct isoforms of a transcription factor were shown to control developmental transitions. lincRNAs were generally lowly expressed at the level of individual cell types, but co-expression clusters provided clues as to their function. Our results highlight insights gained from analysis of expression at the level of individual cell types. •Cell type expression analyses characterize alt splicing and lincRNAs•Splicing tends to remove parts of coding regions from a longer, major isoform•Coordinated alternative splicing appears to regulate differentiation in the root•For the majority of proteins, peptide and major isoform abundance correlate well Li et al. present a comprehensive dataset of gene expression generated using short-read sequencing from individual cell types and developmental zones of the Arabidopsis root, complemented by long-read sequencing and quantitative proteomics analyses. The data in this resource characterize cell-type-specific and developmental-stage-specific alternative splicing and lincRNA expression.