MHC-DAB allele polymorphism in Japanese flounders Paralichthys olivaceus

Polymorphism of the major histocompatibility complex DAB gene in Japanese flounder (Paralichthys olivaceus) was investigated using sequences analysis. In this study, 24 individuals were selected to amplify partial exon1 and intron2, complete intron1 and exon2 of DAB gene. 131 sequences were subsequently used to analyze genetic variation and revealed 31 different sequences, which presented 31 novel alleles belonging to 19 allele major types according to accepted nomenclature rules. Frequency of alleles and numbers of subtype were not distributed equally. There were 50 variable sites in exon2, the average number of nucleotide diversity Pi value of the whole sequences was 0.0618. The nucleotide sequence was corresponded with putative 91 amino acids peptide, 32.97% (30 out of 91) of the amino acid were variable, of which 29 parsimony informative sites were observed. The rates of non-synonymous substitution (dN) were 10.00 times and 1.62 times higher than the rate of synonymous substitution (dS) in the peptide-binding regions (PBR) and non-PBR, respectively. The rate of dN occurred at a significantly higher frequency than that of dS in PBR, dN in PBR was higher than that in non-PBR, but dS in PBR was significantly lower than in non-PBR. In this study, the high ratio of dN/dS value and high allelic diversity observed in flounder suggested a balancing selection in the MHC-DAB gene, which explained the high polymorphism of MHC-DAB gene in Japanese flounder. The number of transitions and tranversions gradually increased with genetic distances, indicating that the MHC-DAB gene might discuss the genetic evolution. Phylogenetic tree was based using NJ method revealed a preliminary phylogeny among 19 MHC-DAB major type of alleles. Frequency of synonym codons were not distributed equally [Acta Zoologica Sinica 54 (5): 909 – 917, 2008].