Exploitation of next generation sequencing technologies for unraveling metabolic pathways in medicinal plants: A concise review

Medicinal plants having high-value and unique active ingredients are attractive in different industries, including pharmaceutical, food and cosmetic sectors. The phytochemicals in these plants are synthesized through diverse biosynthetic pathways including those for mevalonate, shikimic, acetic acid and so forth. Several key enzymes catalyze different reactions in these pathways and convert precursors to final products. Identification of rate limiting enzymes in the biosynthetic pathways of the secondary metabolites and their encoding genes can reveal the bottlenecks of these pathways and ultimately lead us to develop an appropriate breeding strategy for selecting plants possessing desirable and high-quantity active ingredients. Next-generation sequencing methods, in the last two decades, have contributed, in many ways to a more detailed study of medicinal plants and a deeper exploration of these pathways. In this way, an NGS-based whole genome sequencing (WGS) approach and the data it provides, can lead to the development of new high-throughput molecular markers for more effective marker assisted selection (MAS), more accurate QTL and association mappings, easier genotyping by sequencing, a deeper study of phylogenetic relationships, a faster calculation of evolutionary rates of different genes, reconstruction of genetic diversity patterns between plant taxa, and ultimately domestication of wild high-value medicinal plants. In addition, RNA-Seq methods can have a similar application in the plants without a WGS as well as being used for representing the expression profile of the genes in plants with a great impact on functional genomics. NGS-based methods can greatly help medicinal plant researchers to identify genes involved in the biosynthetic pathways of important metabolites including phenolics, terpenoids, alkaloids, glycosides, etc. Subsequently, through metabolic engineering, it would be possible to increase the quantity and quality of sec-ondary metabolites and to develop new medicinal plant cultivars for their exploitation in an industrial scale.