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

The medicinal plant Cnidium officinale (CO) is widespread in Northeast Asia and vulnerable to heat stress. The naturally occurring composition of pharmacological ingredients of CO results in overall physiological consequences; therefore, it is crucial to have a comprehensive understanding of metabolic response to ambient heat in terms of acclimation to estimate how much CO is exposed to threatening environmental conditions.

Transcriptome analysis is critical for understanding the consequences of long-term physiological adaptation of CO to abiotic stress. However, transcriptome analysis on this species, particularly under prolonged stress conditions, has remained limited. We employed a temperature gradient tunnel (TGT) to subject CO to high-temperature exposure for four months, enabling us to observe the cumulative effects of heat and assess its acclimation mechanisms. In the absence of genome sequencing data, we performed de novo transcriptome assembly and compared DEGs from temperature treatment plots of a TGT and a growth chamber (GC). Since interpreting transcriptomic data can be complex, we employed a sequential analytical approach, including DEG clustering, GO enrichment, KEGG pathway mapping, miRNA-target gene analysis, and multiple rounds of RNA sequencing validation. DEGs were classified into two categories: genes exhibiting significant fold changes and genes showing significant count changes rather than fold changes. Then, we analyzed the functional roles of DEGs to determine which pathways respond to ambient and stressful high temperatures and validated the findings through cross-comparison with GC. Additionally, we conducted miRNA analysis to investigate post-transcriptional regulation under high temperatures. CO grown under higher ambient temperatures exhibited slight upregulation of pathways related to protein stability and turnover, ABA biosynthesis, and energy production, such as photosynthesis and oxidative phosphorylation. However, under extreme heat stress, most metabolic pathways were downregulated except for those involved in transcription, translation, oxidative phosphorylation and the biosynthesis of cutin, suberin, and wax.

This study demonstrated that proper clustering of genes based on expression levels and fold changes in two different experimental conditions, along with pathway mapping, may provide a comprehensive understanding of CO's response to heat stress. These insights could contribute to future research on heat tolerance and crop improvement.