Circadian rhythms not only influence the overall daily routine of organisms but also directly affect life activities to varying degrees. Circadian locomotor output cycle kaput (Clock), the most critical gene in the circadian rhythm feedback system, plays an important role in the regulation of biological rhythms. Here, we aimed to elucidate the evolutionary history of the clock gene family in a taxonomically diverse set of vertebrates, providing novel insights into the evolution of the clock gene family based on 102 vertebrate genomes. Using genome-wide analysis, we extracted 264 clock sequences. In lobe-finned fishes and some basal non-teleost ray-finned fishes, only two clock isotypes were found (clock1 and clock2). However, the majority of teleosts possess three clock genes (two clock1 genes and one clock2 gene) owing to extra whole-genome duplication. The following syntenic analysis confirmed that clock1a, clock1b, and clock2 are conserved in teleost species. Interestingly, we discovered that osteoglossomorph fishes possess two clock2 genes. Moreover, protein sequence comparisons indicate that CLOCK protein changes among vertebrates were concentrated at the N-terminal and poly Q regions. We also performed a dN/dS analysis, and the results suggest that clock1 and clock2 may show distinct fates for duplicated genes between the lobe-finned and ray-finned fish clades. Collectively, these results provide a genome-wide insight into clock gene evolution in vertebrates.

昼夜节律不仅影响生物体的整体日常生活，而且在不同程度上直接影响生命活动。昼夜节律反馈系统中最关键的基因——昼夜运动输出周期kaput（Clock）在生物节律的调节中起着重要作用。在这里，我们旨在阐明生物钟基因家族在一组分类上多样化的脊椎动物中的进化历史，为基于 102 种脊椎动物基因组的生物钟基因家族的进化提供新的见解。使用全基因组分析，我们提取了 264 个时钟序列。在叶鳍鱼和一些基部非硬骨鱼鳍鱼中，只发现了两种时钟同种型（时钟1和时钟2）。然而，大多数硬骨鱼的具备三个时钟基因（双时钟1基因和一个时钟2由于额外的全基因组复制基因）。以下同线分析证实了clock1a、clock1b和clock2在硬骨鱼物种中是保守的。有趣的是，我们发现骨舌鱼具有两个clock2基因。此外，蛋白质序列比较表明脊椎动物之间的 CLOCK 蛋白变化集中在 N 端和聚 Q 区。我们还进行了dN/dS分析，结果表明clock1和clock2可能显示叶鳍和射线鳍鱼类进化枝之间重复基因的不同命运。总的来说，这些结果提供了对脊椎动物时钟基因进化的全基因组洞察。