Pan-eukaryotic distribution and deep homology of plant small secreted peptides and their receptors

Small secreted peptides (SSPs) are essential signaling molecules in plants, yet their deep evolutionary origins remained unclear. Here, we integrated sensitive homology searches with rigorous filtering to systematically identify SSP and leucine-rich repeats receptor-like kinase (LRR-RLK) homologs across the EukProt database. We recovered 59 high-confidence SSP homologs from diverse deeply branching eukaryotic supergroups, with protistan sequences consistently placed at the base of phylogenies. Parallel searches recovered 916 LRR-RLKs from non-vascular plant lineages, whereas the SSP-associated XI subfamily was largely confined to Archaeplastida. Co-occurrence of SSPs and LRR-RLKs in 6 lineages, together with bidirectional motif traceability revealing strong purifying selection on core residues, supports a model in which core components of SSP signaling emerged early in eukaryotic evolution and were vertically inherited, with subsequent lineage-specific diversification and co-option during streptophyte evolution. Our study provides a revised evolutionary framework for plant peptide signaling and a broadly applicable strategy for tracing ancient origins of lineage-specific innovations.