Locus-Specific Convergent Evolution and Interchromosomal Rearrangements Contribute to the Diversification of Amniote...

Type I interferons (IFNs) play essential roles in antiviral immune responses. The extensive diversification of type I IFNs into various subtypes and duplicated gene copies has posed significant challenges for evolutionary reconstruction. To address this, we developed the type I IFN sequence composition and structure (IFN-SCOPE) model and gene-network graph degree centrality (GENE-GRADE) algorithm, which transform the discovery of type I IFN evolutionary trajectories into computing the node centrality in its gene networks. Through synteny-guided analysis, we verified that three previously reported evolutionarily conserved type I IFN loci (HACD4, MOB3B, and UBAP2) have maintained chromosomal colocalization across all major amniote lineages. While the MOB3B locus maintained a single IFN-κ ortholog, the HACD4 (IFN-HA) and UBAP2 (IFN-UB) loci showed lineage-specific expansion patterns: IFN-HA proliferated in mammals/reptiles but remained single-copy in birds, whereas IFN-UB expanded in birds but not in other lineages. A phylogenetic analysis revealed that these independently evolved multicopy genes nevertheless clustered into two conserved subgroups (IFN-HA2/HA1 and IFN-UB2/UB1), suggesting convergent functional specialization. Within the IFN-HA and IFN-UB clusters, the single-copy IFN-HA2 and IFN-UB2 genes, positioned at the ancestral ends of their respective genomic arrays, likely represent the progenitor sequences of each locus, where the poorly characterized IFN-ν (rather than IFN-β) is the ancestral form of mammalian IFN-HA subtypes. Furthermore, wet lab evidence revealed type I IFN genes at noncanonical loci resulting from interchromosomal duplication events in tortoises and diving ducks and provided clear evidence that interchromosomal duplications contributed to type I IFN gene diversity. These discoveries advance our understanding of the evolutionary mechanisms that shape type I IFN genes in amniotes and are potentially beneficial for the development of novel type I IFN-based antiviral treatments through comparative immunological approaches.