Integration of single nucleus RNA-seq and bulk RNA-seq reveals gene regulatory networks for vascular connection between parasitic plants and host plants

Single nucleus RNA sequencing (snRNA-seq) offers cellular-level resolution of gene expression patterns in heterogeneous tissues. Here, we applied "VASA-seq (vast transcriptome analysis of single cells using dA-tailing)," a method enabling highly sensitive, full-length, and total RNA-seq analysis of single cells. VASA-seq is compatible with plate-based formats for sorting rare cell populations and droplet microfluidics technology for high-throughput applications and mapping. We employed VASA-seq to perform single nucleus RNA sequencing of haustorial and host cells at 1 day and 7 days post-infection of host plant Arabidopsis thaliana by parasitic plant Phtheirospermum japonicum. Additionally, we integrated bulk RNA-seq data from haustorial and host cells at 1, 3, and 7 days post-infection, as well as bulk RNA-seq data from the same root regions of uninfected parasite and host. This project aims to identify changes in gene expression in both the parasitic plant and the host during different stages of haustorium formation by comparing gene expression profiles at 1, 3, and 7 days post-formation.