Biological rhythms governing metabolic and developmental processes are widespread in organisms, ranging from prokaryotic cyanobacteria to mammals and flower plants. Species of the genus Porphyra sensu lato (e.g., Porphyra, Pyropia, Neoporphyra, etc.) are major red algal seaweeds important to the marine fisheries industry in northeast Asia. Over a long evolutionary history, these seaweeds have adapted to the intertidal zone environment, which is characterized by periodic extreme stresses such as high light, high temperature, high salinity, and drought. However, very little is known about the rhythmic regulation of these seaweeds in response to the shifting environment. In this study, we entrained N. haitanensis thalli with a 12 h/12 h light/dark regime under constant temperature and light intensity, and analyzed the contents of carotenoid constituents and the transcript abundances of genes involved in carotenoid metabolism. Our results clearly demonstrated a 1.52 (zeaxanthin)–2.13 (β-carotene)-fold change between the highest and lowest amounts of carotenoids, and a 7.66 (NhCHYB)–224.00 (NhZISO)-fold change in the expression levels of genes, over the course of a day. These variations indicate that the fluctuations at both metabolic and transcriptional levels of carotenoid metabolism during the light/dark shifting are significant and cannot be neglected, highlighting the need to use a series of parallel non-treated controls instead of a pre-treatment control to avoid the potential confounding effects of the treatment and the diurnal rhythm.
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