TRANSCRIPTOMIC PROFILING AND RNA-SEQ ANALYSIS OF SECONDARY METABOLITE BIOSYNTHESIS PATHWAYS IN MEDICINAL PLANTS UNDER STRESS CONDITIONS: FOCUS ON GENE EXPRESSION PATTERNS (MRNA) REGULATING ALKALOID

Abstract

Alkaloids are diverse chemical defence and signalling molecules used by medicinal plants, however, the transcriptional logic connecting environmental stress to pathway output is disassembled across species and alkaloid classes. This integrative review summarises 40 peer-reviewed studies on RNA sequencing, transcriptome resources, transcription factors, and pathway genetics in Catharanthus roseus, Papaver somniferum, Dendrobium officinale, Nicotiana species, and tropane-alkaloid systems. Evidence was organised around stress perception, hormone signalling, precursor allocation, expression of biosynthetic enzymes, transport and cellular compartmentation. Jasmonate signalling is the most reproducible upstream driver across systems and acts through COI1-JAZ derepression and MYC2-, ERF/ORCA-, bHLH- and WRKY-centred transcriptional modules. However, methyl jasmonate, ethylene, salicylic acid and elicitor treatments not only upregulate all pathway genes, but affect branch selection, timing, tissue specificity and the balance of pathway activators and repressors. Coordinated expression of iridoid and indole branches, ORCA/BIS regulators and late vindoline genes for monoterpenoid indole alkaloid output in C. roseus. Opium poppy gene clusters, fusion enzymes and laticifer-sieve-element specialisation limit benzylisoquinoline alkaloid accumulation. In tobacco, JAZ–MYC2 and NIC2-locus ERFs control nicotine genes, while in D. officinale a broader, partly unresolved alkaloid network can be seen. The synthesis proposes the minimum standards for experimental design and validation and identifies a conserved four-module circuit - signal perception, precursor reallocation, pathway activation and transport/sequestration. Future advances will rely on time-resolved, cell-type-aware, long-read and metabolite-integrated transcriptomics rather than differential expression alone.