title: Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection.
abstract: The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and found that the alleles encode 30 amino acid sequences. A high level of polymorphism in Mimi-DAA was detected in miiuy croaker. The rate of non-synonymous substitutions (d(N)) occurred at a significantly higher frequency than that of synonymous substitutions (d(S)) in the peptide-binding region (PBR) and non-PBR. This result suggests that balancing selection maintains polymorphisms at the Mimi-DAA locus. Phylogenetic analysis based on the full-length sequences showed that the Mimi-DAA alleles clustered into three groups. However, the phylogenetic tree constructed using the exon 2 sequences indicated that the Mimi-DAA alleles clustered into two groups. A total of 22 positively selected sites were identified on the Mimi-DAA alleles after testing for positive selection, and five sites were predicted to be associated with the binding of peptide antigen, suggesting that a few selected residues may play a significant role in immune function.
authors.affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China. Electronic address: tianjunxu@163.com.
authors.forename: Tianjun
authors.initials: T
authors.lastname: Xu
authors.affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Liu
authors.affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
authors.forename: Yueyan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
authors.forename: Zhihuang
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
authors.forename: Tianxing
authors.initials: T
authors.lastname: Liu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000941:Antigens / Q000276:immunology / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics / Q000378:metabolism*; D000949:Histocompatibility Antigens Class II / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D010473:Perciformes / Q000276:immunology*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011485:Protein Binding; D016415:Sequence Alignment
chemical_list: D000941:Antigens; D029941:Fish Proteins; D000949:Histocompatibility Antigens Class II
keywords: Major histocompatibility complex; Miiuy croaker; Polymorphism; Positive selection