Comparative transcriptome analysis reveals ABI3/VP1-WRKY25-STR1 regulatory module linking specialized metabolism with root system development and stress response in Rauvolfia serpentina.

Secondary metabolites play crucial roles in plant defense, development, and ecological interactions, making them valuable for medicinal and agricultural applications. However, the regulatory mechanisms governing their biosynthesis remain incompletely understood. Here, we conduct a meta-analysis of publicly available Rauvolfia serpentina transcriptome data from different plant tissues to investigate secondary metabolite biosynthesis and root system development. Our analysis points to the involvement of distinct biosynthetic routes and associated co-expression networks that may collectively contribute to metabolite production in R. serpentina. The co-expression analysis revealed two putative modules—plum1 and steelblue—that showed a coordinated transcriptional pattern with genes implicated in secondary metabolism. Within these modules, hub-gene analysis identified three key candidates, STR1, ABI3/VP1, and WRKY25, which appear to be linked not only to secondary metabolite biosynthesis but also to aspects of root system development. Subsequent promoter analysis and qRT-PCR validation revealed tissue-specific regulation of WRKY25, STR1, and ABI3/VP1, with significant stress-responsive expression detected primarily in roots, particularly under salicylic acid and drought treatments. This induction pattern reinforces their potential involvement in both metabolite production and broader stress-tolerance mechanisms. Overall, this study provides a useful set of candidate genes and regulatory elements that can be pursued in future functional assays. It also offers preliminary insights into the tissue-specific regulation of secondary metabolite biosynthesis in R. serpentina.