Comparative analysis of MHC class II A gene in <i>Trachinotus mookalee</i> and <i>Trachinotus blochii</i>: Molecular identification and i<i>n silico</i> characterisation

Trachinotus mookalee and Trachinotus blochii are the two commercially important pompano species successfully farmed in aquaculture, and are susceptible to various infectious diseases. As in higher vertebrates, the major histocompatibility complex (MHC) gene superfamily plays crucial role in the adaptive immunity of teleost fishes by mediating the recognition and presentation of pathogen derived antigens to T cells, thereby contributing to disease resistance. The present study reports the identification and in-silico characterisation of the MHC class II A gene in T. mookalee (Trmo-DAA) and T. blochii (Trbl-DAA). The coding region of the target gene in both species was 1026 bp in length, comprising 4 exons and encoding a polypeptide of 241 amino acids.  Phylogenetic analysis revealed that the MHC II A gene of T. blochii is more closely related to Trachinotus ovatus than to T. mookalee. In-silico analysis highlighted that the target gene is involved in the processing and presentation of exogenous antigen, as  supported by domain and motif prediction, Gene Ontologies (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and STRING-based protein-protein interaction networks. The predicted secondary structure (2D)  majorly comprised  random coils and β strands, while the tertiary structure (3D) showed the highest similarity to the MHC class II A protein of Lates calcarifer. Ramachandran plot validation suggested that the predicted 3D structure of Trbl-DAA exhibits  better stereochemical stability than that of Trmo-DAA. These findings provide valuable insights into the molecular and structural characteristics of MHC class II A genes in Trachinotus species and may support future studies on disease resistance and selective breeding. Keywords: Disease resistance, Indian pompano, Selective breeding, Silver pompano, Snubnose pompano, Trmo-DAA, Trbl-DAA