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The chemical diversity of natural products from plants has had a profound and lasting impact on human health with a variety of intriguing structures and biological activities.An understanding of how these molecules are formed would serve a dual role to enable a study of the in vivo function, as well as development of metabolic engineering or synthetic biology production platform to result in a sustainable supply of a drug.Due to lacking the information of genetic background, biochemical pathway elucidation in non-model system has often taken decades to complete.Next-gen sequencing technology enables revolutionary new approaches to understand and regulate valuable secondary metabolism in medicinal plant.Methods using systematic measurements to construct mathematical models of complex biological process from biological components and their interactions are currently being tested in this respect.We present herein a broadly applicable rapid biosynthetic gene discovery method using large datasets derived from genomics, transcriptomics, proteomics, and metabolomics to investigate the functions of key gene and transcript factor involved in metabolic network.Case study of gene discovery involved in phenylpropanoids biosynthesis and pathway regulation to engineer high level of active compounds in Isatis indigotica will be presented.