Transcriptome Profiling of Phloem Sieve Elements in the Arabidopsis Root at Single Cell Resolution

The stereotyped patterning and unidirectional growth of the of the primary Arabidopsis thaliana root meristem allows the study of tissue differentiation with unprecedented resolution. Sieve elements (SE), the cells in the phloem transporting photosynthates over long distances, show a unique morphogenesis which includes cell elongation, cell wall thickening, sieve plate formation and the degradation of organelles, including the nucleus. There are approximately 20 cells along the differentiation gradient from the first stem cell to the enucleating and immediately afterwards functional cell. To study the differentiation processes, we created several protophloem specific fluorescence reporter lines allowing the distinction of cells in different developmental stages. Using these lines, we performed Fluorescence Activated Cell Sorting (FACS) and subsequent RNA sequencing. We are investigating with an extremely high temporal resolution and a high sequencing depth the expression patterns within the 20 cells utilizing single cell and bulk sorting approaches, respectively. This allows us to identify novel SE regulators, infer a regulatory network and unravel the connections between known regulatory components of protophloem SE differentiation. Using SEs in the Arabidopsis root as a model, this is, to our knowledge, the first full description at a single cell resolution of the entire differentiation process in plants.