Pan-NLRome Analysis of Cultivated Tomato and Wild Solanum Relatives Reveals an Open Immune Repertoire Dominated by Spatially Dispersed Homologs.

Background/Objectives: Nucleotide-binding leucine-rich repeat (NLR) proteins are major intracellular immune receptors involved in effector-triggered immunity. However, the evolutionary diversity and genomic organization of NLR repertoires remain incompletely characterized in Solanaceae crops and their wild relatives. This study aimed to investigate the pan-NLRome landscape and evolutionary patterns of tomato and related species. Methods: A comparative pan-NLRome analysis was performed across five angiosperms, including cultivated tomato (Solanum lycopersicum) and four related species (Solanum chilense, Solanum lycopersicoides, Solanum pimpinellifolium, and Arabidopsis thaliana). NLR genes were identified using an integrated HMMER- and BLASTp-based pipeline, followed by chromosome anchoring, orthogroup (OG) classification, phylogenetic analysis, spatial organization analysis, and evaluation of associations with long terminal repeat (LTR) retrotransposons. Results: A total of 1566 chromosome-anchored NLR genes were assigned to 150 OGs. Core OGs represented 25.3% of total OG diversity but contained a large proportion of NLR genes. Rarefaction analysis indicated continuous accumulation of novel OGs with increasing species sampling, supporting an open pan-NLRome structure. Phylogenetic analysis identified 18 NLR subfamilies, with SF_03 and SF_01 together accounting for approximately 79% of NLR genes. Dispersed homologs represented the predominant spatial arrangement pattern, accounting for 85.1% of NLR gene pairs across Solanaceae species. Conclusions: This study provides a comparative genomic framework for understanding NLR diversity and evolution in tomato and related Solanum species, highlighting the dynamic expansion and spatial organization of plant immune receptor repertoires and providing valuable resources for resistance gene discovery.