Leveraging Biodiversity Collections for Venom Gene Evolutionary Research

Venom evolution has traditionally been investigated using proteomic and transcriptomic approaches, which have provided critical insights into toxin composition and function but remain constrained by uneven taxonomic and geographic sampling. These methods rely on fresh tissue and targeted field collections, biasing venom discovery toward medically relevant, easily accessible, or frequently encountered species, while underrepresenting the extensive ecological and biogeographic diversity present in many venomous lineages. Within Cnidaria, sea anemones exemplify this gap: despite exhibiting at least 16 characterized toxin families with diverse functions, large portions of their phylogenetic diversity remain unsampled. Here, we introduce a complementary framework that leverages whole-genome shotgun sequencing and reference-guided annotation using museum and biodiversity collections, focusing on Clade Stichodactylina as a model system. By standardizing genome-based toxin annotation, we demonstrate high concordance and sequence conservation relative to proteomic and transcriptomic datasets, validating whole-genome data as a robust resource for venom gene discovery. Analyses of phospholipase A2 (PLA2) toxins further reveal high numbers of orthologs coupled with strong purifying selection, rejecting a simple birth-and-death model of venom evolution for this family. Together, our results highlight the value of genome-enabled approaches for expanding venom research beyond traditional sampling paradigms and underscore that evolutionary dynamics of venom genes are highly clade- and family-specific, cautioning against generalized models of venom evolution.