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

Area of Science:

• Genomics
• Evolutionary Biology
• Immunogenetics

Background:

• Major histocompatibility complex (MHC) genes are crucial for immune response and known for high vertebrate polymorphism.
• The specific drivers and extent of MHC polymorphism remain incompletely understood across many species.

Purpose of the Study:

• To characterize the polymorphism of MHC class II genes in Atlantic herring.
• To investigate the extent and potential mechanisms driving MHC II diversity in a highly abundant vertebrate.

Main Methods:

• Utilized 29 haploid genome assemblies from long-read sequencing data.
• Analyzed nine identified MHC II loci across four chromosomes in Atlantic herring.

Main Results:

• Discovered nine MHC II loci in Atlantic herring, with three exhibiting extreme polymorphism.
• Observed high sequence diversity, especially at peptide-binding sites, and significant copy number variation.
• Herring MHC class II genes are among the most polymorphic documented in vertebrates.

Conclusions:

• Atlantic herring possess exceptionally diverse MHC class II genes.
• High polymorphism suggests strong balancing selection acting on these immune genes in herring populations.