Genetic Diversity and Evolutionary Dynamics of Two RLRs Genes in Bovine Species

The C-terminal domain (CTD) of the DEAD box polypeptide 58 (DDX58) and of the interferon induced with helicase C domain 1 (IFIH1) genes, is involved in detecting of viral nucleic acids and subsequently triggering of the cascade-like activation process of genes encoding type 1 interferon and pro-inflammatory cytokines. Here, we investigated genetic diversity and evolutionary dynamics in the CTD of these two genes in five bovine species and two buffalo species. The extent of genetic diversity in DDX58 gene fragment was higher as compared to IFIH1 among the species of Bovini tribe. The neutrality tests in considered species had non significant deviation from neutral expectation which indicative of either weak positive or negative selection for both genes. Codon-based Z-tests depicted positive selection in coding haplotypes from the DDX58, but pinpointed towards purifying selection in those from IFIH1. Additional analyses of the full coding sequences of mammalian DDX58 and IFIH1showed that DDX58 has been subject to positive selection with one inferred positively selected site in the CTD region, whereas IFIH1 has been under strong selective constraints. The contrasting evolutionary forces governing the two genes may reflect their different functional importance in detection of virus and innate immune response.