title: Evolutionary analysis of TLR9 genes reveals the positive selection of extant teleosts in Perciformes.
abstract: The innate immune system can recognize non-self through pattern recognition receptors. Toll-like receptors were the best-known members of these receptors, and they could sense, recognize, and bind pathogen-associated molecular patterns. TLRs played an important role in innate immune system and were conserved in both invertebrate and vertebrate lineages. Thereinto, TLR9 could detect unmethylated CpG motifs in dsDNA and was expected to undergo coevolution with its microbial ligands. It was known that aquatic and terrestrial organisms dwelled in different environments which contained different pathogens, and they had to adapt to their local environmental conditions. Therefore, we collected TLR9 genes from invertebrate to vertebrate to further explore whether the huge differences between aquatic and terrestrial environments affected the TLR9s evolution between aquatic and terrestrial organisms. Molecular evolution analysis detected positively selected sites in the ancestral lineages of vertebrates, teleosts, and Perciformes but not in the ancestral lineage of mammals. In PAML, site model revealed that extant mammalian TLR9 genes underwent positive selection. However, the positive selection of extant teleosts appeared primarily in Perciformes in which there were 14 positively selected sites. Among these sites, two of them were located on the amino acid insertions of the leucine-rich repeats which could create DNA binding sites, three were found on the convex surface which might possibly affect the ﬂexibility of the TLR solenoids, and six were located on the β-face of concave surface which contained the ligand-binding sites of the TLR solenoids. In other ML methods, we also found three sites under selection that coincided with the codons identiﬁed by M8 and these sites were all located in LRRs. The diverse aquatic and terrestrial environments might possess different pathogens to make the living organisms adapt to their local environmental conditions. The positive selection on LRRs in TLR9s of Perciformes might be associated with the adaptation to the rapidly evolving pathogens in the water.
authors.affiliation: Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, 105 Wenhua Road, Zhejiang Province, Zhoushan 316000, PR China.
authors.forename: Zhihuang
authors.initials: Z
authors.lastname: Zhu
authors.forename: Yuena
authors.initials: Y
authors.lastname: Sun
authors.forename: Rixin
authors.initials: R
authors.lastname: Wang
authors.forename: Tianjun
authors.initials: T
authors.lastname: Xu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010473:Perciformes / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012641:Selection, Genetic; D016415:Sequence Alignment; D051217:Toll-Like Receptor 9 / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D051217:Toll-Like Receptor 9
keywords: Leucine-rich repeats; Molecular evolution; Perciformes; Positive selection; Toll-like receptor 9