Molecular evolution of aspartic protease gene family in vertebrates

Aspartic proteases are a gene superfamily with diverse functions in vertebrates, including pepsinogens (Pgs), the precursors of the major gastric enzyme pepsin. Despite their physiological importance, the evolutionary history of this gene family has been studied only in a fragmented manner. Here, we conducted comprehensive phylogenetic and genomic synteny analyses using whole-genome data from 75 vertebrate species to systematically elucidate the molecular evolution of aspartic protease genes. We identified Pg genes in cartilaginous fishes (elasmobranchs) for the first time, demonstrating that Pgs originated in the gnathostome ancestor. Pregnancy-associated glycoprotein (PAG) genes showed explosive expansion in cetartiodactyla but underwent secondary reduction in cetaceans. Cathepsin E (ctse), predicted to be the ancestral gene of Pgs, was also found in cartilaginous fishes and non-teleost ray-finned fishes (e.g., gar, bichir, bowfin), but was independently lost in multiple lineages, including teleosts, ruminants, vampire bats, and several stomach-less species. Our results reveal complex patterns of lineage-specific tandem gene duplication, lineage-specific expansion, and convergent gene loss, providing an evolutionary framework for understanding the functional diversification of aspartic proteases in relation to feeding strategies, digestive physiology, and reproductive adaptations in vertebrates.