Single-cell and spatial dissection of host-microbe interactions

In multicellular organisms, individual cells interpret a multitude of developmental and environmental signals through unique gene regulatory mechanisms, leading to highly diverse cellular responses. A comprehensive understanding of tissue function necessitates investigating these complex and heterogeneous gene regulatory patterns, all while maintaining the native three-dimensional (3D) tissue context. In this seminar, I will cover two main topics: (1) the use of single-cell multiomics and spatial transcriptomics in studying spatiotemporal dynamics of gene regulatory mechanisms at the single-cell resolution in the model plant Arabidopsis thaliana, and (2) the development of PHYTOMap, a novel method for multiplexed single-cell 3D spatial gene expression analysis in whole-mount plant tissue. I will present how these methodologies allow for unprecedented resolution in studying interactions between plants and microbes.