LncRNA-driven Immune Networks Bridge PTI and ETI Responses to Reinforce MYMIV Resistance in Vigna Mungo

Mungbean Yellow Mosaic India Virus (MYMIV) induced yellow mosaic is a highly destructive disease that severely compromises Vigna mungo production. Although host defence involves large-scale transcriptional reprogramming, regulatory role of lncRNAs in sculpting this multilayered resistance remains largely unexplored. Here, we report the first comprehensive atlas of lncRNAs in MYMIV-challenged resistant (VM-R) and susceptible (VM-S) genotypes, revealing distinct molecular signatures associated with contrasting disease tolerance phenotypes. Comparative analysis revealed 637 and 574 differentially expressed lncRNAs (DELs) in VM-R and VM-S, respectively, predominantly functioning in cis to regulate 858 and 932 genes, with fewer acting in trans on 360 and 313 targets. Functional enrichment revealed distinct patterns, with VM-R preferentially activating SAsignalling, ROS homeostasis, and hypersensitive response, that bridge Pattern-Triggered Immunity (PTI) and Effector-Triggered Immunity (ETI) to reinforce antiviral defence, whereas VM-S exhibited extensive metabolic reprogramming. Weighted Gene Coexpression Network Aanalysis (WGCNA) further delineated DELs into 27 coexpression modules, with MEgreen and MEpurple strongly associated with VM-R and VM-S, respectively, highlighting genotype-specific co-expression frameworks. Competing endogenous RNA (ceRNA) network uncovered a unique regulatory architecture in which 7 lncRNAs act as target mimics, sequestering 7 miRNAs to modulate expression of 11 targets in VM-R and 7 target mRNAs in VM-S. We propose that in VM-R, the ceRNA pair VmLnc.2876.15-miR5675 activates TIR-NB-LRR mediated defence, whereas reduced VmLnc.3702.1 in VM-S fails to sequester miR482, lowering RING/U-Box levels and compromising immunity. Our machine learning models identified a distinct set of DEL and ceRNA module with strong predictive potential for distinguishing resistant from susceptible interactions. qPCR validation confirmed these key DELs, their targets, and associated ceRNA elements, highlighting their role in lncRNA-mediated immune regulation. Collectively, these findings illuminate the mechanistic roles of lncRNAs in coordinating MYMIV resistance, offering promising strategies to boost crop resilience and yield.