Single nucleus transcriptome analysis of Arabidopsis thaliana roots infected with Phytophthora. capsici

Understanding how plant roots coordinate immune responses at the cellular level is key to unraveling host–pathogen interactions. Using single-nucleus RNA sequencing (snRNA-seq) of Arabidopsis thaliana roots 24 hours after Phytophthora. capsici ( P. capsici )inoculation, we captured the transcriptional landscape of early infection at single-cell resolution. Four libraries (two infected and two mock-treated) were generated with approximately 26,000 high-quality nuclei with consistent sequencing depth and viability. A reference-based pipeline distinguished host and pathogen transcripts, enabling species-resolved mapping and host-focused single-nucleus transcriptomic analysis. Integration and clustering identified 12 transcriptionally distinct root cell types, encompassing major tissues such as the meristem, cortex, endodermis, and vasculature. Cluster-specific marker analysis confirmed cell-type identities, while differential expression and Gene Ontology enrichment revealed a global transcriptional shift from metabolic and translational processes in mock samples to defense-, stress-, and pathogen-response pathways upon infection. Hormone-related enrichment indicated broad salicylic acid activation across root tissues, spatially confined ethylene signaling in vascular-associated clusters, and localized jasmonic acid responses in cortex and phloem. Together, these results provide a high-resolution view of Arabidopsis root immunity, highlighting a coordinated yet tissue-specific defense architecture in which salicylic acid underpins systemic protection, ethylene modulates vascular defense, and jasmonic acid contributes targeted reinforcement during early P. capsici infection.