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

Innate immune IFNs most likely emerged during tetrapod evolution from fish (2, 5, 9, 10, 12) . Cross-species genome-wide annotation verified that fish only have a few ancestral introncontaining IFNs; however, multiple IFN genes in each amniote species are mostly intronless (2, 5, (9) (10) (11) (12) . The intronless type I IFNs in amniotes appear to have arisen from a retroposition event that is assumed to have replaced the original IFN locus by the integration of intron-spliced RNA and, thus, favored subsequent gene duplication and family expansion adaptable to rapidly evolving viruses and functional divergence (2, (9) (10) (11) (12) . We have genome-wide examined IFN genes across the genome sequences of nearly 120 representative species of vertebrates, and identified the emergence and expansion of intronless IFNs in amphibians (10) (11) (12) . For example, in two Xenopus genomes, 13-16 intron-containing IFN genes (of both type I and type III IFNs) exist that retain intron-containing gene structure as fish IFN genes, and 24-37 intronless IFN genes, indicating the emergence and expansion of intronless IFN genes in amphibians rather than in reptiles as previously assumed (Figure 1 and Supplemental Excel Sheet) (10) (11) (12) . Although type I IFN genes kept evolving to be intronless in reptiles and birds, the gene diversification process became less active than in amphibians, as most reptile and bird species contain several IFN genes similar to those in the fish but they are mostly, or nearly intronless (2, 10-12). Among the analyzed bird species, the domestic chicken and duck have the most 9-10 IFN-coding genes. Dramatic IFN gene diversification further occurred in several mammalian species. With regard to IFN-coding genes, ungulate species such as cattle (Bos taurus/indicus) and pigs (Sus scrofa) have nearly 60 predictable IFN-coding genes as well as more than a dozen pseudogenes (8, 9, 12) . Other mammalian species show IFN gene expansion with more than 20 predictable IFN-coding genes including the ungulates domestic sheep, horses, and yak, the house mouse and many primate species including human and pongo (7) . Most other wild mammalian species generally have 7-16 predictable IFN-coding genes, except two underground-living mole rats (H. glaber and F. damarensis) that have most redundant compositions of type I IFN coding genes comparable to fish. In summary, cross-species and genome-wide definition of IFN genes in vertebrate species determined previously unknown molecular complexity of IFN expansion in Amphibian (10), Chiroptera, Rodent (except the two moles) and domestic ungulate species especially pigs and cattle (2, (8) (9) (10) . This revises the linear-increasing pattern of IFN molecular evolution as previously proposed along amniotic evolution (12) . Several gene expanding-surges are particularly FIGURE 1 | Molecular evolution and diversification of type I IFNs and IFN-ω subtype in representative vertebrate species. Functional IFN gene numbers are annotated from released genomes of representative species and plotted along the phylogenetic order according to NCBI Taxonomy at http://www.ncbi.nlm.nih.gov/Taxonomy. Several major events including the retroposition leading to emergence of intronless IFNs in amphibians, and expansion of IFNs in amphibians, livestock, bats, and mice are shown (8) (9) (10) . evident in amphibians, domestic birds and ungulates, as well as some rodent species, which illustrates a lineage, even speciesindepe