Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

Abstract

The Major Histocompatibility Complex (MHC) plays a central role in vertebrate adaptive immunity, yet its genomic architecture remains poorly characterized in many evolutionary model systems, including the Neotropical Midas cichlid Amphilophus citrinellus. Here, we integrate chromosome-level functional genome annotation, transposable element (TE) profiling, transcriptomics, phylogenetics, molecular selection analyses, and protein structural modeling to characterize its MHC repertoire. We identified 298 MHC-related loci across 18 chromosomes, including 30 MHC-I genes, 15 MHC-IIA genes, and 20 MHC-IIB genes, together with antigen-processing and regulatory components. MHC-I and MHC-II genes were located on different chromosomes, consistent with the MHC non-linkage pattern characteristic of many teleosts. Gene duplication and phylogenetic patterns support birth-and-death evolution, resulting in a structurally diverse repertoire with broadly conserved protein domains. TE distribution varied across MHC genomic regions, suggesting a potential contribution to genomic diversification. Molecular selection analyses detected positive selection in MHC-I and IIB genes, whereas MHC-IIA showed more limited evidence of positive selection. Expression patterns varied across tissues, with relatively high expression of several MHC genes in the spleen and thymus, while structural models retained characteristic MHC folds. Phylogenetic analyses placed previously characterized MHC sequences with broader multilocus repertoire, suggesting that population level diversity may reflect both allelic polymorphism and variation among paralogous loci. Together, these findings provide a comprehensive chromosome-resolved characterization of the MHC repertoire in a Neotropical cichlid and establish a genomic framework for investigating immune gene diversification during the Midas cichlid radiation.