Phylogeny-informed nomenclature of chicken corneous beta protein (beta-keratin) genes

Abstract Corneous beta-proteins (CBPs; historically known as beta-keratins) are major structural proteins of sauropsid epidermal appendages, including feathers, claws, and scales, yet CBP gene nomenclature and annotation remain inconsistent across genome assemblies and species. Using modern broiler and layer chicken reference genomes, we identified 271 protein-coding CBP genes. Comparative analyses revealed substantial variation among CBP groups in gene redundancy, annotation concordance, and protein sequence diversity. These differences were particularly pronounced in feather-associated CBP loci, including a chromosome 27 region exhibiting reduced local synteny and extensive assembly-specific gene annotations. Despite these challenges, phylogenetic analyses consistently resolved eight major CBP families and supported development of a standardized phylogeny-informed nomenclature system. Application of this framework to turkey and zebra finch demonstrated that phylogeny-informed classification can be extended across birds and avoids problems associated with expression- and morphology-based naming systems, which are used inconsistently across species. In the genomic regions examined, chicken-derived gene names could be assigned to 67 of 78 (87.2%) turkey CBPs and 34 of 40 (85.0%) zebra finch CBPs. Together, these findings establish a phylogeny-informed nomenclature for chicken CBP genes and demonstrate its applicability across avian species, providing a foundation for consistent gene naming and comparative studies of CBP evolution in birds.