Spotted Gar and the Evolution of Innate Immune Receptors

Abstract

The resolution of the gar genome affords an opportunity to examine the diversification and functional specialization of immune effector molecules at a distant and potentially informative point in phylogenetic development. Although innate immunity is effected by a particularly large number of different families of molecules, the focus here is to provide detailed characterization of several families of innate receptors that are encoded in large multigene families, for which orthologous forms can be identified in other species of bony fish but not in other vertebrate groups as well as those for which orthologs are present in other vertebrate species. The results indicate that although teleost fish and the gar, as a holostean reference species, share gene families thought previously to be restricted to the teleost fish, the manner in which the members of the multigene families of innate immune receptors have undergone diversification is different in these two major phylogenetic radiations. It appears that both the total genome duplication and different patterns of genetic selection have influenced the derivation and stabilization of innate immune genes in a substantial manner during the course of vertebrate evolution.

The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes

“…Our previous analyses of spotted gar immune genes revealed shared characteristics with those of both teleosts and tetrapods, but left important aspects of the ray-nned sh immunogenome unresolved 7,44 . For a comprehensive understanding of holostean immune genes, we surveyed the bow n genome and a newly generated bow n immune tissue transcriptome (Supplementary Note 4).…”

“…Toll-like Receptors (TLRs) provide initial immune responses to infection in animals 60 . Bow n possesses 20 TLR genes from all six families, twice the number of human TLRs 61 , more than the 16 functional spotted gar TLRs 7,44 , and almost on par with the more than 20 teleost TLR genes 62,63 ( Supplementary Fig. 10, Supplementary Table 12, Supplementary Note 4).…”

Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system

“…AMCP sequences) for NITR sequences, we employed spotted gar NITR I domains (Wcisel et al 2017) as queries for BLASTP searches (e value cutoff < 1e-15) as the high rate of sequence evolution in NITR V domains limits their utility for effective homology searches over deep evolutionary time scales. In order to identify bowfin NITR transcripts, we used the candidate NITR sequences encoded by the genes described above and all reported spotted gar NITR I domains (Wcisel et al 2017) as queries for tBLASTn searches (e values <1e-10) against immune tissue RNA-seq from bowfin 0039 (Thompson et al 2021) and from bowfin available from PhyloFish (Pasquier et al 2016) ( Supplementary Note 1 ). Resultant protein sequences were manually inspected and those lacking an Ig domain or found to encode Ig light chain proteins were excluded.…”

The Spotted Gar: Genomic Journeys into a Lost World

“…Wcisel, Ota, Litman, and Yoder () investigated the gar immune gene repertoire and found that although the gar innate immune receptors share more sequence similarities with teleost sequences, their genomic organization often resembles that possessed by tetrapod genomes.…”

“…Kawasaki et al (2017) expanded their investigations of the evolution of the SCPP protein family involved in the formation of mineralized tissues such as bone, dentine, enamel, and ganoin, finding that the SCPP family is larger in gar than any other vertebrate studied thus far. Wcisel, Ota, Litman, and Yoder (2017) investigated the gar immune gene repertoire and found that although the gar innate immune receptors share more sequence similarities with teleost sequences, their genomic organization often resembles that possessed by tetrapod genomes. Beaudry et al (2017) used the spotted gar genome as starting point to illuminate the evolutionary history of non-visual opsin genes among vertebrates.…”