Sequence Variation and Gene Duplication at MHC DQB Loci of Baiji (Lipotes vexillifer), a Chinese River Dolphin

• Published in: Journal of Heredity
• Main Authors: Yang, G., Yan, J., Zhou, K., Wei, F.
• Format: Text
• Language: English
• Published: Oxford University Press 2005
• Subjects: Article; Beluga; Beluga whale; Beluga*; Delphinapterus leucas; Monodon monoceros; narwhal*
• Online Access: http://jhered.oxfordjournals.org/cgi/content/short/esi055v1; https://doi.org/10.1093/jhered/esi055

The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an important role in the recognition of parasites. Baiji ( Lipotes vexillifer ) is one of the most endangered species in the world. Its wild population has declined to fewer than 100 individuals and has a very high risk of becoming extinct in the near future. In this study we present a first step in the molecular characterization of the MHC class II DQB locus of baiji by nucleotide sequence analysis of the polymorphic exon 2 segments. In the examined 172 bp sequences from a group of 18 incidentally captured or stranded individuals, 48 variable sites were determined and 43 alleles were identified. No deletion, insertion, or exceptional stop codon was detected, suggesting these alleles function in vivo. Phylogenetic reconstruction using neighbor joining, as implemented in the computer software Molecular Evolutionary Genetics Analysis (MEGA), divided the 43 alleles into two monophyletic lineages. Seven nucleotide and four amino acid diagnostic sites were found to be different between, but shared within the lineage. Substitutions of amino acids tend to be clustered around sites postulated to be responsible for selective peptide recognition. In the peptide-binding region (PBR) of the DQB locus, the average number of nonsynonymous substitutions per site is greater than that of synonymous substitutions per site (0.1962 versus 0.0256, respectively). Nucleotide and amino acid sequences both showed a relatively high level of similarity (nucleotides 90.6%; amino acids 80.6%) to those of beluga whale ( Delphinapterus leucas ) and narwhal ( Monodon monoceros ). Amino acid sequences did not share motifs with human and other primate species, but showed a similar motif to that of cattle DQB1 sequences. Thus the alleles were identified as DQB1 -like loci. Three to seven alleles were found in each individual, suggesting the existence of four or more DQB loci in the baiji ...