A single-nucleus multiome profiling reveals the regulatory programs driving plant nematode-induced syncytium

Plant-parasitic cyst nematodes induce the formation of specialized feeding structures, known as syncytia, within host roots by orchestrating extensive transcriptional and epigenetic reprogramming. Here, we generated parallel single-nucleus RNA-seq and ATAC-seq libraries from fully developed Heterodera schachtii-induced syncytia on Arabidopsis roots. We analyzed high-quality transcriptome and chromatin profiles independently and in an integrated framework. We identified multiple transcriptomic cell states, several of which were highly syncytium-enriched and spanned vascular and cortical identities. Differential expression analysis identified hundreds of syncytium-enriched genes, and pseudotime trajectory inference points to potential compartmentalization or functional heterogeneity of syncytium nuclei, consistent with the possibility of distinct transcriptional programs within or between mature syncytia. Joint clustering of snATAC-seq with snRNA-seq delineated syncytium-unique chromatin accessibility landscapes, with several cell states exhibiting extensive open chromatin linked to upregulated genes. Motif enrichment across these accessible regions highlighted cis-regulatory elements mainly for AP2, bZIP, bHLH, MYB, and TCP transcription factors and identified functionally validated members of these families as candidate regulators of syncytium identity. Our study establishes a multiome atlas of syncytial cells and uncovers the regulatory programs driving nematode feeding site maintenance, as well as transcriptionally distinct nuclear states that may reflect functional specialization within or between the syncytia.