De novo transcriptome assembly and gene expression analysis of Cnidium offinale under high- temperature conditions

Abstract

Background The medicinal plant Cnidium officinale (CO) is widespread in Northeast Asia and vulnerable to heat. Therefore, its habitat and cultivation area move to a cool environment, such as the high-altitude northern area. Results Due to absent genome sequencing data, we performed de novo transcriptome assembly and compared it with an existing sequencing database. About 90% of CO genes were similar to Daucus carota. We found 16 novel and 24 nearly identical or homologous miRNAs with reported miRNAs. We tried to comprehensively understand the physiological response of CO to ambient and stressful high temperatures compared with differentially expressed genes (DEG) from different temperature treatment plots of temperature gradient tunnel (TGT) and growth chamber (GC). We classified DEGs into three categories: newly appeared or disappeared genes, the genes that showed significant fold changes, and the genes that showed significant count rather than fold changes. Afterward, we mapped DEGs among the metabolic pathways to determine which pathways respond to ambient and stressful high temperatures. CO grown in higher ambient temperature conditions showed slightly upregulated membrane fluidity-related pathways, glutathione, and overall energy metabolism (e.g., photosynthesis, carbon fixation, and oxidative phosphorylation). Under heat stress, CO showed a strong response in various metabolic pathways, with most being downregulated except for several defense-related pathways and respiration, including oxidative phosphorylation and cutin, suberin, and wax biosynthesis. Recently, transcriptome analysis has demonstrated its role in understanding the overall response of plant samples under a specific condition; however, in most cases, the data after analysis are complicated and challenging to discover, although some pinpoint-level understanding might be advantageous. Conclusion This study demonstrated that a proper clustering of genes based on expression level and fold changes in two different experimental conditions and pathway mapping may be useful for reaching a comprehensive conclusion.