The serpins constitute a superfamily of proteins that fold into a conserved tertiary structure and employ a sophisticated, irreversible suicide-mechanism of inhibition. More than 6000 serpins have been identified, occurring in all three forms of the life - the eukaryotes, the prokaryotes and the archea. Vertebrate serpins can be conveniently classified into six groups (V1 - V6), based on three independent biological features - gene organization, diagnostic amino acid sites and rare indels. In the present work, the phylogenetic relationships of serpins from Nematostella vectensis, Strongylocentrotus purpuratus, Ciona intestinalis, four fish species, frog, chicken and mammals were investigated, using gene architecture analyses and stringent criteria for identification of orthologs. With some deviations, all vertebrate serpin genes fit into one of the six exon/intron gene classes previously identified, dating the existence and maintenance of these gene organizations before or close to the divergence of fishes. Group V1 and V2 gene families underwent rapid adaptive radiation along the lineages leading to mammals as indicated by an up to nine-fold increased number of family members, accompanied by a rapid functional diversification. In contrast, gene groups V3 to V6 display a rather conservative evolution with little changes since the divergence of fishes and the other vertebrates. The orthology assessment indicates that all vertebrates are equipped with a subset of strongly conserved serpins with functions that can be clearly correlated with basic vertebrate-specific physiology.

None of serpin genes from C. intestinalis shares a common exon-intron architecture organisation with any of the vertebrate serpin gene classes, nor was it possible to identify orthologs of vertebrates. The lack of gene architecture similarity and the complete absence of orthology between urochordate and vertebrate serpins indicate that major changes with bursts of character acquisition must have occurred during evolution of serpins in the time interval separating urochordates from chordates, indicating massive intron gains or losses and events providing C and N-terminal sequence extensions characteristic for today's vertebrate serpins. Lancelets and sea urchin genomes, in contrast, share one orthologous serpin with vertebrates. Rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group V3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait.

Phylogenomic comparisons show that, after establishment of canonical exon-intron patterns in the serpin superfamily at the dawn of vertebrate evolution, multiple intron acquisition events have occurred during diversification of a lineage of actinopterygian fishes. The novel introns were acquired within a limited time interval (on an evolutionary timescale), and no such events were observed in other groups of vertebrates. Examination of the sequences flanking the intron insertion points revealed that the genetic requirements for acquisition of novel introns might be less stringent than previously suggested. Finally, we argue that genome compaction, a phenomenon associated with the fish lineage depicting preferential intron gain, might promote intron acquisition.