Dynamic regulation of NLR networks reveals a strongly inducible NLR-like gene during the Pinus–Fusarium circinatum interaction

Abstract Nucleotide-binding leucine-rich repeat (NLR) receptors play a central role in effector-triggered immunity, yet their diversity, regulation and evolutionary dynamics in conifers remain poorly understood. We investigated the NLR repertoire of Pinus pinaster during infection by the pathogen Fusarium circinatum , identifying 193 NB-ARC–containing genes expressed throughout infection. TIR-NLRs (TNLs) represented the largest subfamily, whereas helper-type RPW8-NLRs (RNLs) were comparatively rare. Most NLRs were transcriptionally repressed, but a subset displayed strong late induction, revealing four distinct temporal expression clusters. Phylogenetic analyses showed clear separation of major NLR clades but no correspondence between evolutionary relationships and transcriptional patterns, indicating extensive regulatory diversification. Among induced genes, on gene ( PpRG ) displayed exceptionally strong upregulation. Expression profiling across Pinus species showed conserved PpRG induction following F. circinatum infection, whereas lesion severity did not correlate with expression levels. In P. pinaster , PpRG responded specifically to stem-infecting pathogens ( F. circinatum , Diplodia sapinea ), but not to foliar pathogens, endophytic fungi, methyl jasmonate, or drought. Functional and phylogenetic analyses indicate that PpRG is related to NLR-like proteins, although its classification remains unresolved. Together, our results reveal a dynamically regulated NLR repertoire in P. pinaster and identify PpRG as a strongly induced, stem‑associated gene with potential value as a candidate biomarker associated with immune signalling during interactions with canker-causing pathogens. Key message A dynamically regulated NLR network is revealed in Pinus pinaster , identifying a strongly inducible defence-related gene with NLR-like features.