Recurrent Duplication of the REST-NOA1 Locus Reveals a Hotspot of Regulatory Evolution Across Even-Toed Ungulates

Abstract

Gene duplication is a major source of evolutionary novelty, yet recurrent duplication of the same genomic locus across independent lineages remains understudied. Using a chromosome-scale assembly and de novo annotation of the North American bison (Bison bison), we investigated the mechanisms underlying immune-system diversification in ungulates. Comparative genomics of bison, cattle, elk, and 13 mammalian species identified a large segmental duplication encompassing the regulatory genes REST and NOA1. Although similar duplications were present in 14/16 species examined, phylogenetic analyses revealed that duplicated genes cluster within species rather than across taxa, indicating repeated independent origins rather inheritance from a common ancestor. To characterize the evolutionary consequences of this duplication, we integrated transcriptomics from six tissues with weighted gene co-expression and comparative protein clustering. We identified extensive structural divergence among duplicated copies of REST and NOA1, including domain losses, truncations, and expression partitioning across tissues, consistent with functional divergence following duplication. Comparative analyses revealed substantial remodeling of immune-related genes in bison, including BOLA class I molecules, T-cell receptor genes, leukocyte immunoglobulin-like receptors, and regulators of immune signaling. These modifications included domain rearrangements, novel sequence insertions, and lineage-specific duplications associated with immune-related expression networks. Together, these findings identify the REST-NOA1 locus as a recurrent hotspot of segmental duplication in ungulates and demonstrate how repeated duplication, structural divergence, and regulatory partitioning contribute to genome evolution. These results suggest that immune system diversification in bison and related species has been shaped not only by sequence evolution but also by recurrent remodeling of regulatory pathways and antigen-recognition pathways.