Plants have evolved specialized secondary metabolite biosynthetic pathways for the synthesis of structurally and functionally complex small molecules, which aid in the growth and development of the plants but are not required for the survival of the plants, themselves. Plant secondary metabolites play a crucial role in plant-environment interactions for adaptation to diverse and inconstant surroundings. They are synthesized in different organs/tissues or plants specific at particular developmental stages in response to various biotic and abiotic stimulus. Recent advances in genetic engineering have enabled not only to increase the concentration of desired metabolites, but it also allows to introduce novel biosynthetic pathways to a variety of species for the enhanced nutritional or commercial value. Integration of transcriptomics, proteomics, and bioinformatics has enabled the identification of novel biosynthetic pathways involved in the biosynthesis of specialized metabolites. In this study we present the comprehensive knowledge of development in RNA sequencing studies for the metabolic engineering of plant natural products.