Unique Composition of Intronless and Intron-Containing Type I IFNs in the Tibetan Frog Nanorana parkeri Provides New Evidence To Support Independent Retroposition Hypothesis for Type I IFN Genes in Amphibians

Abstract

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Xenopus Interferon Complex: Inscribing the Amphibiotic Adaption and Species-Specific Pathogenic Pressure in Vertebrate Evolution?

“…There was a total of 437 positions in the final dataset. In contrast to the previously known several fish-like intron-containing amphibian IFNs, recent studies revealed that amphibians are unique to have both fish-like intron-containing and amniotic intronless IFNs, which molecularly and immunologically stamp their amphibiotic position in vertebrate evolution [12,13,16]. Legends and Abbreviations: IFN-I, type I IFNs (including amniotic intronless IFNA, IFNB, IFNE, IFNK, IFNW, respectively, for the genes of IFN-α, -β, -ε, -κ, -ω; and diverse amphibian intron-containing, XaIFN For instance, extensive analysis of current genome assemblies of Xenopus tropicalis and Xenopus laevis at NCBI (https://www.ncbi.nlm.nih.gov/genome/?term=Xenopus) and Xenobase (http://www.…”

“…We therefore updated the current repertoire of IFN gene loci in X. tropicalis: The co-existence of 14 Figure 1) [13]. A new study in a Tibet frog species (Nanorana parkeri) reinforced the co-existence of both intron-containing and intronless IFN genes in amphibians [16]. However, the expansion of antiviral IFN genes in different amphibian species, especially the intronless ones, seems species-independent.…”

“…There was a total of 437 positions in the final dataset. In contrast to the previously known several fish-like intron-containing amphibian IFNs, recent studies revealed that amphibians are unique to have both fish-like intron-containing and amniotic intronless IFNs, which molecularly and immunologically stamp their amphibiotic position in vertebrate evolution [12,13,16]. Legends and Abbreviations: IFN-I, type I IFNs (including amniotic intronless IFNA, IFNB, IFNE, IFNK, IFNW, respectively, for the genes of IFN-α, -β, -ε, -κ, -ω; and diverse amphibian intron-containing, XaIFN or XtIFN, and intronless XaIFNX or XtIFNX, listed here); IFN-III, type III IFNs (including amniotic intron-containing IFNL gene for IFN-λ; and amphibian intron-containing XaIFNL or XtIFNL, and intronless XaIFNLX or XtIFNLX, listed here); SCCA 1, Scyliorhinus canicula (catshark) ancestral IFN-I; SCCA L, Scyliorhinus canicula (catshark) ancestral IFN-III; Dr, Danio rerio (zebrafish); Gg, Gallus gallus (chicken); Hs, Homo sapiens; Xa, Xenopus laevis; Xt, Xenopus tropicalis; Group designation: 1 and 7 & 8, intron-containing ancestral IFN-I (7 & 8) and IFN-III (1); 2, intron-containing IFN-III in amniotes; 3 and 4, amphibian intron-containing IFN-III (3) and IFN-I(4); 3X and 4X, intronless amphibian IFN-III (3X) and IFN-I (4X); 5X and 6X, intronless IFN-I in amniotes.…”

“…We annotated IFN gene families across 110 vertebrate genomes, and showed that IFN genes, after originating in jawed fishes, had several significant evolutionary surges regarding the numbers of IFN-coding genes and subtypes in some species of amphibians, bats, and ungulates (particularly pigs and cattle of livestock) [13][14][15]. Here, we review the newly identified IFN molecular evolution and expansion in amphibians [12,13,16].…”

“…The evolution of intronless (or single-exon) IFN genes and further molecular diversification in amniotes are signature events in IFN evolution [11][12][13][14][15][16]. However, our understanding of this Figure 1.…”