Genomic structure, polymorphism, and expression analysis of the spotted scat Scatophagus argus major histocompatibility complex class I alpha gene

The complete complementary DNA (cDNA) sequence of the major histocompatibility complex (MHC) class I α gene in Scatophagus argus was obtained by homology-based cloning and rapid amplification of cDNA ends polymerase chain reaction (PCR. The intron sequences, polymorphism, and tissue expression of this gene were then analyzed. The gene cDNA sequence is 2020 base pairs (bp) in length, including a 86-bp 5′-untranslated region (UTR), 866-bp 3′-UTR and 1068-bp open reading frame. It contains seven exons and six introns, of which there are two types of the fourth intron with respective lengths of 655 and 691 bp; it also has microsatellite (T)n fragments, and the sixth intron has a separate 3′-UTR. From 42 individuals, 20 alleles of the class I α-chain gene were identified, called here “Scar-UA*0101–Scar-UA*2001,” which demonstrate high polymorphism. Reverse transcription-PCR analysis shows its expression in ten tissues, with high expression levels in the liver, spleen, and kidney, and low levels of expression in the stomach, intestines, and muscle. A tree depicting the molecular relationships built using the neighbor-joining method shows that Scatophagus argus has a close genetic relationship to Perciformes fish such as Sparus aurata, Dicentrarchus labrax, and a more distant relationship to salmonid and cyprinid fishes, amphibians, birds, and mammals.