Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium.
VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium.
Plant J. 2021 Jul;107(1):315-336. doi: 10.1111/tpj.15291. Epub 2021 May 18.
Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23 328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24 h. Phylostratigraphic analysis found that rhythmic genes are enriched in highly conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall-associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for the study of diurnal regulation in photosynthetic eukaryotes.
沿海地区仅占海洋表面积的 0.03%，但其每年的总初级生产力估计贡献了 20%。硅藻经常在沿海沉积物中占主导地位，那里的光照条件因昼夜和潮汐周期的相互作用而发生很大变化。在这里，我们报告了对运动底栖硅藻 Seminavis robusta 的广泛的昼夜转录谱分析实验。近 90%（23328 个）表达的蛋白编码基因和 66.9%（1124 个）表达的长基因间非编码 RNA 表现出显著的表达波动，主要在夜间以 24 小时的周期分相。系统发育分析发现，节律基因富含高度保守的基因，而硅藻特有的基因主要与午夜表达相关。将遗传和生理细胞周期标记与硅耗竭数据相结合，揭示了潜在的新的硅藻特有的硅细胞壁相关基因家族。此外，我们观察到 1752 个基因具有显著的半日（12 小时）周期性，而推测的昼夜转录因子的扩展可能反映了对高度不可预测的外部条件的适应。总之，我们的研究结果为硅藻对底栖环境的适应提供了新的见解，并为研究光合真核生物的昼夜调控提供了有价值的资源。
