Genomic analysis and adaptive evolution of the RIG-I-like and NOD-like receptors in reptiles

Abstract

Pattern recognition receptors (PRRs) play a crucial role in the host's innate immune system. Among the PPRs, the RIG-I-like (RLRs) and NOD-like receptors (NLRs) are two important subgroups. To understand the role of RLRs (RIG-I, MDA5, LGP2) and NLRs (NOD1, NLRC3, NLRX1, NOD2) in reptilian evolution, we identified six genes from reptilian genomes. A total of 168 putative genes were identified from 28 reptile species, including 141 intact genes, 25 partial genes and two pseudogenes. Interestingly, the NOD2 gene was absent in all reptile species. Phylogenetic results showed that all genes were divided into four major clades corresponding to their traditional taxonomic groups, indicating that these genes are conserved in reptiles. Evolutionary analyses detected positive selection in six genes. Most of the positively selected sites (50/76) were located in known functional domains, reflecting their critical and particular contributions to host defense during reptilian evolution. Branch model analysis showed that NLRs were under different evolutionary forces, while the RLRs were not, suggesting that semiaquatic species and terrestrial species faced different environmental pathogens, leading to different adaptations. Moreover, the positively selected sites identified in MDA5 using the branch-site model among semiaquatic reptiles, suggested their involvement in adaptation to semiaquatic environments.