Abstract: Degenerate primer was designed according to the conserved part of MHC-Ⅱα gene sequences of other fishes, and the techniques of homology cloning and RACE PCR were used to clone the MHC-Ⅱα gene from cobia Rachycentron canadium). The cDNA sequence and amino acid sequence were analyzed, and the differences between MHC-Ⅱα amino acid sequence of cobia and other species were compared. QRT-PCR assay was developed to assess the mRNA expression of MHC-Ⅱα in normal tissues and the tissues after injected with LPS. The results showed that the full length cDNA of MHC-Ⅱα comprises 998 bp with a 5′untranslated region (UTR) of 53 bp, a 3′UTR of 234 bp and an open reading frame (ORF) of 711 bp, which encoding a polypeptide of 236 amino acid residues with a predicted molecular weight of 25.94 ku and theoretical isoelectric point of 4.39. The putative protein showed homology varying from 25.0% to 69.5% compared to some known MHC-Ⅱα amino acids in other fish, mouse （Mus musculus） and human （Homo sapiens）, respectively. The protein sequence showed that all the important features: leader peptide, α1, α2 and CP/TM/CYT regions, and conserved cysteines. Real-time PCR indicated MHC-Ⅱα gene expressed in all detected tissues with different expression level. High expression was detected in head kidney, gill, moderate expression in spleen and intestine, and low expression in heart, brain and muscle. MHC-Ⅱα expression in the head kidney decreased after LPS stimulation.

Key words: cobia (Rachycentron canadum); MHC-Ⅱα; full length cDNA; mRNA expression