Characterization of immunoglobulin loci in Pongo abelii and Pongo pygmaeus: Insights from multi-genome annotation and IMGT-based curation

Antibodies, or immunoglobulins (IGs), are central to the vertebrate adaptive immune system, yet the genomic architecture of IG loci remains poorly characterized in many nonhuman primates. In this study, we present the first comprehensive genomic analysis of the IG loci (IGH, IGL, and IGK) in two critically endangered orangutan species; Pongo abelii (Sumatran orangutan) and Pongo pygmaeus (Bornean orangutan) across seven genome assemblies. Using IMGT-standardized biocuration framework combined with read-level structural validation, we identified previously undocumented haplotype-specific variation, including multigene duplications and deletions, and expansions of variable gene families within the analyzed assemblies. Recombination signal sequence and switch region analyses revealed conserved regulatory motifs with potential implications for V(D)J recombination and class-switch recombination. These findings underscore the complexity and evolutionary adaptability of IG loci in great apes and highlight the value of orangutans as key references for understanding immune system evolution in the Hominidae lineage.