Cross-Species Genome-Wide Analysis Reveals Molecular and Functional Diversity of the Unconventional Interferon-? Subtype

Shields, Lauren E.; Jennings, Jordan; Liu, Qinfang; Lee, Jinhwa; Ma, Wenjun; Blecha, Frank; Miller, Laura C.; Sang, Yongming

Genetic polymorphisms of a few nucleotide residues are frequently found in the promoter or coding regions of type I IFN genes (14, 28, 29) . We and others have found that striking differences in IFN activity is associated with simple polymorphic mutations (14, 28, 29) . This implies a genomic mechanism of IFN-system evolution, which is critical in the arms race with evermutating viruses to create a novel antiviral genotype. Regarding porcine IFN-ω genes, on the basis of the 11 porcine IFN-ω coding genes determined in the reference swine genome assembly (Sscrofa11.1, NCBI), extensive sequencing of IFN genes isolated from the DNA pool of 400 pig blood samples allowed us to identify 3-7 SNP of each IFN-ω functional gene, with the IFN-ω5 gene having the maximal 7 SNP identified in that DNA pool (14) . These several porcine IFN-ω5 polymorphic isoforms (Figure 3) , which only differ from each other by few residues, showed dramatic activity differences (Figures 6-9 ; next) (9, 13, 14, 24) . (7-9, 17, 18, 27) . Generally, we detected segregation of IFN-ω subtype in birds, but the definitive formation of multi-gene IFN-ω was detected in the genomes of mammals from all Orders except Monotremes, Marsupials, and Rodents. Further phylogenic analysis indicated that IFN-ω molecules from individual Order or Genus might share one common progenitor, as shown in Figure 2 for the clustered phylogenic clades and in Figure 4 for peptides that share >86% of identity. It was common to observe that IFNω molecules from one species are phylogenically closer to the orthologs from other species of the same Family/Genus than those from the same species (Figures 2, 4) . For the mammalian genus/species that have multiple genes of IFN-ω subtype, we observed that IFN-ω peptides such as in bats, moles, shrews, and elephants are formed into two major sub-clusters; however, it is primarily only one sub-cluster (with one to several "outliers") such as in swine and bovine species (Figures 2, 4) . In addition, several clusters of IFN-ω peptides contain IFN-ω peptides from animals of different Genus/Family, such as that of the ungulatemix (alpaca, camel, and bioson) and the RBH-mix (rhino, bat, and horse) clusters (Figure 4, upper panel) . In contrast to the potential evolutionary progenitor shared in mammalian species, IFN-ω genes undergo reduction or expansion independently in each animal species, which are especially evident, such as IFN-ω gene expansion in swine and bovine species (Figure 4 , bottom panel).