Wolffia australiana Time of Day scRNA-seq

Single cell genomics has permitted a new level of resolution in the examination of molecular and cellular dynamics. It allows global, parallel assessment of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the 24-hour light-dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced plant, the semi-aquatic Wolffia australiana to understand dynamics of cell expression in these contexts at the whole plant level. We examined single cell resolution RNA-Ssequencing data and found Wolffia divides into four principal clusters of tissue types representing the above and below water-situated parenchyma and epidermis. While these tissues share similarity at the transcriptome level with model plants, they display distinct adaptations that Wolffia has made for the aquatic environment. Assessing this simplified biological system temporally at two times of day (TOD), we identify additional TOD-responsive genes previously overlooked in whole plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in a cell-specific manner even in this simplified system. Intriguingly, distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of remarkably few genes, characterizing Wolffia as a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes. Wolffia provides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.