The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.

中文翻译：

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穗草中昼夜基因调控的种间分析确定了已知和新颖的调控基序。

昼夜节律时钟驱动内源性的24小时节律，使生物能够适应整个昼夜（昼夜）周期中环境的可预测和反复变化并做好准备。拟南芥中生物钟的许多组成部分已在功能上进行了表征，但对草种（包括玉米和高粱等主要作物）中生物钟的了解相对较少。基于蛋白质同源性和昼夜基因表达模式的比较研究表明，草中某些预测的时钟成分的功能与拟南芥中的那些相同，而其他则有所不同。我们分析了三种圆锥花序草高粱，玉米，谷子和谷子揭示了核心昼夜节律时钟基因和整个转录组的表达的保守和发散演变。我们发现，与拟南芥相比，这些草中的几类核心生物钟基因的拷贝数不同，但除了玉米旁系基因外，大多数都表现出蛋白质序列和昼夜表达模式的保守性。我们通过鉴定27,196个直系同源基因的子集的昼间共表达簇来预测玉米，高粱和谷子之间共享的保守的顺式调控基序。在此分析中，一种基于Cochran–Mantel–Haenszel的方法来控制背景变化，该方法在预期的共同昼夜调节基因的启动子区域中预期的和新颖的6–8个核苷酸基序均显着富集，并预计将在共同的生理活动中起作用。这项研究说明了跨类兜铃草物种中同系直系同源基因的昼夜节律和昼夜调节网络的差异性和保守性。此外，保守的局部调控序列有助于这些昼夜调控网络的结构，这些网络产生昼夜基因表达的保守模式。