title: Identification of 48 full-length MHC-DAB functional alleles in miiuy croaker and evidence for positive selection.
abstract: Major histocompatibility complex (MHC) molecules play a vital role in the immune response and are a highly polymorphic gene superfamily in vertebrates. As the molecular marker associated with polymorphism and disease susceptibility/resistance, the polymorphism of MHC genes has been investigated in many tetrapods and teleosts. Most studies were focused on the polymorphism of the second exon, which encodes the peptide-binding region (PBR) in the α1- or β1-domain, but few studies have examined the full-length coding region. To comprehensive investigate the polymorphism of MHC gene, we identified 48 full-length miiuy croaker (Miichthys miiuy) MHC class IIB (Mimi-DAB) functional alleles from 26 miiuy croaker individuals. All of the alleles encode 34 amino acid sequences, and a high level of polymorphism was detected in Mimi-DAB alleles. The rate of non-synonymous substitutions (dN) occurred at a significantly higher frequency than that of synonymous substitutions (dS) in the PBR, and this result suggests that balancing selection maintains polymorphisms at the Mimi-DAB locus. Phylogenetic analysis based on the full-length and exon 2 sequences of Mimi-DAB alleles both showed that the Mimi-DAB alleles were clustered into two major groups. A total of 19 positive selected sites were identified on the Mimi-DAB alleles after testing for positive selection, and 14 sites were predicted to be associated with antigen-binding sites, which suggests that most of selected sites are significant for disease resistance. The polymorphism of Mimi-DAB alleles provides an important resource for analyzing the association between the polymorphism of MHC gene and disease susceptibility/resistance, and for researching the molecular selective breeding of miiuy croaker with enhanced disease resistance.
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. Electronic address: tianjunxu@163.com.
authors.forename: Tianjun
authors.initials: T
authors.lastname: Xu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002681:China; D019143:Evolution, Molecular; D005802:Genes, MHC Class II; D010473:Perciformes / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012641:Selection, Genetic; D016415:Sequence Alignment
keywords: Allele; Major histocompatibility complex (MHC); Molecular evolution; Polymorphism; Positive selection