# Dual RNA-seq analysis reveals differences in defensive lncRNA expression in Pinus spp. with varying susceptibility to Fusarium circinatum

## TL;DR

This study uses dual RNA-seq to explore how lncRNAs in pine trees and a pathogen differ between resistant and susceptible species during infection.

## Contribution

The first lncRNA catalogues for P. pinea and F. circinatum, revealing non-coding regulatory differences in resistance and susceptibility.

## Key findings

- P. radiata and P. pinea showed distinct lncRNA expression patterns linked to defense and metabolic processes.
- F. circinatum lncRNAs were associated with transcriptional control and toxin production during infection of resistant hosts.
- Resistant pine lncRNAs clustered into defense-related modules, while susceptible ones were linked to photosynthesis.

## Abstract

Long non-coding RNAs (lncRNAs) are emerging regulators of plant immunity, but their roles in conifer-pathogen interactions remain largely unexplored. We applied a dual RNA-seq approach to resistant Pinus pinea and susceptible P. radiata challenged with Fusarium circinatum at 4 dpi, and concurrently profiled fungal lncRNAs.

Using a conservative multi-tool pipeline, we identified 8,783 lncRNAs in P. radiata, 5,255 in P. pinea, and 1,020 in F. circinatum. Pine lncRNAs displayed canonical features (shorter length, fewer/shorter exons, intergenic dominance) and limited primary-sequence conservation. Differential expression analysis revealed 37 (P. radiata) and 34 (P. pinea) infection-responsive lncRNAs. Predicted cis targets in P. radiata were enriched for energy/redox and gibberellin-related functions, whereas P. pinea targets pointed to TCA/redox and translation control. Weighted gene co-expression analysis placed P. radiata lncRNAs in defence-like modules without significant infection association, while P. pinea lncRNAs clustered into two modules with opposite associations to infection: one that increased and was enriched for immunity, flavonoid biosynthesis, and cell-wall processes, and another that decreased and was linked to photosynthesis and chloroplast functions. On the pathogen side, infection of the resistant host triggered distinct F. circinatum lncRNAs linked to transcriptional control and putative cis activation of cell-wall–degrading and toxin-biosynthetic genes, alongside down-regulation near ergosterol-biosynthetic loci. By contrast, during infection of the susceptible host, species-associated modules were dominated by translation-related functions.

Together, these results define a non-coding regulatory layer that differentiates resistance and susceptibility strategies in the Pinus–F. circinatum pathosystem, provide the first lncRNA catalogues for P. pinea and F. circinatum, and deliver testable candidates for functional validation and biomarker development in forest disease management.

The online version contains supplementary material available at 10.1186/s12870-026-08182-w.