Genome-wide identification, phylogeny, and expression of IL17 receptor genes in common carp (Cyprinus carpio) and grass carp (Ctenopharyngodon idella)

To gain a better understanding of the evolution and action mode of the IL17R family in common carp (Cyprinus carpio) and grass carp (Ctenopharyngodon idellus), the two representative species of Cyprinidae, we analyzed them with the method of comparative genomics and bioinformatics. Sequence alignment and annotation were conducted in the genome database of common carp and grass carp as well as the analysis of genetic structure and phylogeny respectively. Finally, gene expression analysis was performed in 12 different tissues of these two species. We identified and characterized nine and five IL17R homologues. Along with genes annotation and nomenclature, phylogenetic analysis built on amino acid sequences of the IL17R proteins in 12 species showed highly conservative and no specific genes in teleosts. Comparative genomics showed that there was no significant increase in IL17 receptor genes in most teleosts compared with tetrapods. Nevertheless, except for IL17RB genes, all of the members showed extensive gene duplications, leading to nine IL17R genes in common carp. Expression analysis of different tissues showed that the functions of different gene copies were differentiated after the whole genome duplication. Studies have shown that an additional round of duplication, also named teleost-specific (TS) WGD, or the 3R WGD, took place in the common ancestor of all extant teleosts. After duplication, one of the two redundant copies of a gene should theoretically have the freedom to degenerate and become lost from the genome without consequence. Also, it was generally hypothesized that, compared to other teleost, common carp had undergone additional whole genome duplication (the 4R WGD). The comprehensive estimation based on whole genome datasets suggested that the latest WGD event occurred around 8.2 MYA. Therefore, we postulated that the significant expansion of IL17R genes in the common carp genome may be the result of this additional WGD, which could have caused a sudden doubling of the IL17R genes and the IL17RB had been lost in their evolution history with the reason that the functions of genes were redundant and conservative. Expression profiling showed that most of the IL17R genes were expressed in a more-or-less tissue-specific fashion.