Compact genomic architecture of the axolotl MHC region: setting the record straight

The Major Histocompatibility Complex (MHC) is a gene-dense genomic region essential to adaptive immunity, exhibiting both conserved features and lineage-specific rearrangements across jawed vertebrates. Amphibians, as basal tetrapods, offer critical insights into MHC evolution; however, research has largely focused on anurans (e.g., Xenopus), while urodeles remain understudied, primarily due to their exceptionally large genomes. With recent advances in sequencing technologies, chromosome-scale assemblies for urodeles are now becoming available, opening new opportunities to explore their MHC architecture. Yet, the MHC region remains notoriously challenging to annotate due to its complexity, high polymorphism, and dynamic evolutionary history. For instance, the initial annotation of the axolotl (Ambystoma mexicanum) MHC relied heavily on synteny with mammalian genomes, which led to an overestimation of its size and misinterpretation of its structure. These inaccuracies have fueled evolutionary debates regarding the ancestral genomic structure of the MHC. Here, we present a comprehensive re-annotation of the axolotl MHC, revealing a typical organization found in tetrapods other than eutherian mammals: core MHC region with several, expressed MHC class I genes, tightly linked to their antigen processing genes, and to single loci of MHC class II genes. Contrary to the previous report, class I and class II genes are not separated by class III genes, and the overall MHC region is relatively compact (by axolotl genome standards). These findings correct earlier misconceptions and emphasize the need for annotation strategies that reflect the complex and lineage-specific nature of genomic regions rich in immune genes.