Long read genome unravels MHC I genomic architecture, evolution, and diversity loss in Gubernatrix cristata

Abstract

The major histocompatibility complex (MHC) genes are vital for the adaptive immune response in vertebratesand are widely used in conservation genetics to represent adaptive variation. Accurate genotyping of MHCalleles is essential for effective conservation, particularly for endangered species like the yellow cardinal(Gubernatrix cristata). However, the absence of locus-specific primers and the highly repetitive nature ofthese genes present a technical limitation when using short-read sequencing technologies. We producedthe first high-quality long-read reference genome for the yellow cardinal. This genome reveals sustainedhigh genome-wide heterozygosity despite inbreeding, with homozygosity patterns and effective populationsize estimates indicating a long-term decline. We identified seven genomic MHC-I loci, while ampliconsequencing with non-locus specific primers had not confirmed more than two MHC-I loci. Our study also revealed mismatches in primer binding sites across multiple loci, emphasizing the need for high-quality, longread genomic data to understand the genomic architecture of MCH and to accurately assess locus specificMHC variation.