Abstract The Period genes ( Per ) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events of Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3 , which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa. Significance The Period ( Per ) genes play essential roles in the circadian rhythm in animals. In this study, we comprehensively investigated the evolutionary diversification of the three types of Period genes in vertebrates. As a result, we observed a rapid evolution and sub-functionalization of these genes, especially adaptive diversification signatures in the protein-binding region, which plays a crucial role in regulating circadian rhythms. This underscores the fine-tuned contribution of Per genes in the biological clock’s precision and adaptability across various vertebrate taxa.

Functional and regulatory diversification of circadian rhythmperiodgenes during the evolution of vertebrates