Receptor-module diversity and lineage-specific expansion of the LRR-RLP pan-gene family in tomato and allied wild relatives

Leucine-rich repeat receptor-like proteins (LRR-RLPs) mediate cell-surface perception through modular ectodomains and membrane-proximal signalling complexes. Although tomato wild relatives harbour extensive genomic diversity, how LRR-RLP lineages, receptor modules, copy number and chromosomal context vary across the tomato clade remains unresolved. We reconstructed an LRR-RLP pan-gene family from the primary proteomes of 76 accessions, identifying 3,798 candidates in 97 OrthoFinder-based orthogroups (OGs). No OG was detected in every accession under the annotation, detection and clustering criteria used here; restricting the panel to 72 sect. Lycopersicon accessions also yielded no strict core OG. The full panel comprised 14 soft-core, 42 shell, six cloud and 35 private OGs. Shell OGs represented 43.3% of OGs and 61.8% of candidates. Independent reciprocal-best-hit and synteny checks supported pairs in 40 OGs and flagged six nominally private OGs. Among 6,024 island domains (IDs), terminal ID+4LRR recurred across the panel, extending earlier cross-species observations. Communities spanning four or five comparison groups contained 93.6% of ID events. C3 and eJM–TM–cJM module trees showed partial topological discordance, although two classification boundaries had weak bootstrap support. Comparable accession-level multi-copy OG burdens involved different receptor lineages; tandem and proximal relationships accounted for 86.5% of detected within-OG duplication pairs. Heinz-relative local structural variants affected 28 of 3,539 callable candidates. RLP-OG0013 had the highest median pairwise Ka/Ks (1.55), a descriptive divergence signal requiring lineage-aware selection tests. In two Botrytis cinerea inoculation time courses, 43 candidates from 27 OGs were differentially expressed. LA2574 reads were quantified against LA1777 reference genes, permitting OG-level integration but no inference of LA2574 genomic copy number. The tomato LRR-RLP pan-gene family combines recurrent receptor architectures with accession-dependent lineage representation and copy expansion. Its OG-level genomic and expression summaries identify candidates for genotype-matched tests of pathogen recognition and resistance.