Functional transcriptomic analysis and drought-induced regulation of secondary metabolism in Artemisia ludoviciana Nutt

Artemisia ludoviciana Nutt. is an aromatic medicinal plant, widely used in Mexican folk medicine for the traditional treatment of different diseases, including diabetes. Numerous secondary metabolites related to its medicinal properties have been identified, of which monoterpenoids, sesquiterpenes, and flavonoids are the most significant. Despite extensive research, transcriptomic evidence supporting secondary metabolite synthesis in A. ludoviciana remains limited. Functional transcriptomics provides the molecular basis for understanding how coordinated gene expression drives metabolite synthesis in A. ludoviciana at a given time and condition. RNA sequencing of A. ludoviciana leaves was performed using a single pooled RNA-seq library as an exploratory functional transcriptomic approach, generating 8.4 GB of transcriptomic data. After de novo filtering and assembly of the raw data, 52,561 transcripts were generated, of which 29,854 (56.79%) were annotated against public databases using Blast2GO. Further KEGG pathway analysis identified transcripts putatively associated with major plant secondary metabolite biosynthesis pathways. Gene expression of candidate flavonoid-related genes (CHI, F3’MO, FSI, and F3’OMT) was assessed by qRT-PCR in Artemisia ludoviciana. Samples were collected following water stress, with soil moisture content approximately 25%. Drought conditions significantly reduced relative water content (32.78%), total chlorophyll, and carotenoids. This was accompanied by an increase in hydrogen peroxide accumulation (265%), indicating oxidative stress in the plant. The total phenolic and flavonoid content also decreased under these conditions. However, gene expression analysis showed increased transcript abundance of putative flavonoid-related genes, suggesting an active response of the plant’s flavonoid pathway to water stress. Such effects might reflect metabolic constraints and flavonoid turnover under drought stress. This work provides valuable insights into the functional gene annotation, the biosynthetic pathways of secondary metabolites, and the molecular response of A. ludoviciana to drought stress. It serves as a basis for further research into the molecular mechanisms underlying the synthesis and accumulation of bioactive compounds in Artemisia ludoviciana. In addition, it supports the development of strategies to maintain or enhance the species’ medicinal properties.