Unheralded high MHC class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing

Although major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, we still lack a clear understanding about the extent of polymorphism and selection mechanisms dominantly driving it. Here, we use 29 haploid genome assemblies resolved by long-read sequencing to characterize MHC II genes in Atlantic herring, a pelagic fish and one of the most abundant vertebrates on Earth. We found nine MHC II loci in total distributed on four chromosomes, three of which were extremely polymorphic because of high sequence diversity, in particular at peptide binding sites, along with high copy number variation. This study reveals that the herring MHC class II genes are among the most, if not the most, polymorphic so far described in vertebrates.