Transcriptome sequencing with nanopore technology for acquiring a deeper understanding of abscisic acid regulation of secondary mechanisms in Salvia miltiorrhiza

The phytohormone abscisic acid (ABA) plays a central role in mediating plant responses to environmental stresses. As a part of the stress response, the biosynthesis of certain secondary metabolites can be triggered by ABA. Salvia miltiorrhiza is a well-known medicinal plant that produces many biologically active components, such as tanshinones and salvianolic acid B. In this study, for the first time, we investigated S. miltiorrhiza transcriptome variations in response to ABA treatment by using Oxford Nanopore Technology (ONT). More than 76 Gb of clean ONT reads were generated from twelve cDNA libraries , and a total of 22,233 genes were detected. The expression pattern of approximately 50% of these genes was changed upon ABA induction, including most genes involved in ABA biosynthesis and ABA signal transduction , which suggests that in plants, multiple ABA signaling-induced cellular processes respond in a coordinated fashion to environmental stress. In addition, in S. miltiorrhiza leaves, ABA can change alternative splicing outputs mainly by reducing intron retention (IR) events through posttranscriptional splicing, which can quickly enhance protein biosynthesis to help plants cope with environmental stresses. Interestingly, ABA can upregulate the expression of genes involved in salvianolic acid biosynthesis but exerts a lesser effect on tanshinone biosynthesis, which indicates the different roles of these two classes of metabolites in response to environmental stresses. A better understanding of the ABA regulatory mechanism and ABA-triggered secondary metabolism will boost our ability to improve herb quality through molecular-assisted breeding, abiotic stress management and chemical manipulation with ABA-based bioactive agents. • ABA can activate key genes involved in ABA biosynthesis and signal transduction. • ABA can enhance protein biosynthesis by triggering posttranscriptional splicing. • ABA can promote salvianolic acid biosynthesis. • ABA exerts a lesser effect on tanshinone biosynthesis.