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Simplification of circadian rhythm measurement using species-independent time-indicated genes

Tanigaki, Yusuke, Higashi, Takanobu, Takayama, Kotaro, Nagano, Atsushi J., Honjo, Mie N., Tezuka, Ayumi, Kamitani, Mari, Fukuda, Hirokazu
Current plant biology 2019
Arabidopsis thaliana, Lactuca sativa, Solanum lycopersicum, circadian rhythm, crop management, genes, nucleotide sequences, photosynthesis, plant growth, transcriptome, transcriptomics
The circadian rhythm varies among species, and the distribution of common circadian rhythm-related genes in plants is not yet clearly understood. In this study, we analyzed the transcriptome data from plants of three different species (Solanum lycopersicum, Arabidopsis thaliana, and Lactuca sativa) and their circadian rhythms. Homology of the gene sequences was analyzed. Thirty genes containing time information were found to be common among the three species studied and were used to measure the circadian rhythm. Because 22 of these 30 genes were associated with photosynthesis, we suggest that light control could be used to regulate the circadian rhythm. Currently, a high-cost transcriptome analysis is required for the measurement of circadian rhythm; however, our results showed that it was possible to reduce the number of target genes to 30 and, hence, to reduce the cost of the analysis. Our findings will enable easier estimation of circadian time, which, in turn, will facilitate environmental control for plant growth through better control of circadian time, thus facilitating better crop management practice.