Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Needles Across Different Seasons.

(Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the needle ultrastructure was damaged, and the chlorophyll content and / were significantly ( < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMsDEGs were significantly ( < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, , and in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (, and ) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of and the extraction of its metabolites.