Genome-wide characterization of NBS-encoding genes in Luffa cylindrica and their putative roles in disease resistance

Sponge gourd ( L. cylindrica Mill.), a crucial dual-purpose crop in the Cucurbitaceae family, faces severe yield losses due to diseases like Fusarium wilt and Tomato leaf curl New Delhi virus (ToLCNDV) infection. The NBS-LRR (Nucleotide-Binding Site–Leucine-Rich Repeat) gene family, core components of plant Effector-Triggered Immunity (ETI), plays a vital role in pathogen defense. This study conducted a comprehensive genome-wide analysis of the NBS-LRR gene family in Luffa cylindrica using bioinformatics tools and transcriptome data. A total of 89 NBS-LRR genes were identified and classified into seven subfamilies: TIR(Toll/Interleukin-1 Receptor)-NBS-LRR(TNL) (15), TIR-NBS(TN)(16), CC (Coiled-Coil))-NBS-LRR(CNL)(8), CC-NBS (CN) (14), NBS(N)(23), NBS-LRR (NL) (10), and RN(RPW8-NBS) (3). These genes showed irregular distribution across 12 chromosomes, with the highest density on Chr08. Phylogenetic analysis revealed five primary clades, reflecting evolutionary relationships among subfamilies. Conserved domain and motif analysis indicated intra-subfamily conservation and inter-subfamily divergence, with all members containing the core NB-ARC domain. Promoter cis -acting element analysis identified 65 elements, with light-responsive and hormone/defense-stress-responsive elements being predominant, suggesting involvement in multiple biological processes. Intra-species synteny analysis found two homologous gene pairs between Chr02 and Chr06, while inter-species analysis showed closer evolutionary ties with cucumber (18 orthologous pairs) than Arabidopsis (1 ortholog) and no orthologs with rice. Tissue-specific expression analysis revealed highest expression in roots, and disease response analysis identified six genes associated with ToLCNDV resistance and nine genes linked to Fusarium wilt resistance. These findings provide valuable resources for understanding the molecular basis of disease resistance in L. cylindrica and accelerating disease-resistant breeding.