Plants produce an array of specialized metabolites, including chemicals that are important as medicines, flavors, fragrances, pigments and insecticides. The vast majority of this metabolic diversity is untapped. Here we take a systematic approach toward dissecting genetic components of plant specialized metabolism. Focusing on the terpenes, the largest class of plant natural products, we investigate the basis of terpene diversity through analysis of multiple sequenced plant genomes. The primary drivers of terpene diversification are terpenoid synthase (TS) "signature" enzymes (which generate scaffold diversity), and cytochromes P450 (CYPs), which modify and further diversify these scaffolds, so paving the way for further downstream modifications. Our systematic search of sequenced plant genomes for all TS and CYP genes reveals that distinct TS/CYP gene pairs are found together far more commonly than would be expected by chance, and that certain TS/CYP pairings predominate, providing signals for key events that are likely to have shaped terpene diversity. We recover TS/CYP gene pairs for previously characterized terpene metabolic gene clusters and demonstrate new functional pairing of TSs and CYPs within previously uncharacterized clusters. Unexpectedly, we find evidence for different mechanisms of pathway assembly in eudicots and monocots; in the former, microsyntenic blocks of TS/CYP gene pairs duplicate and provide templates for the evolution of new pathways, whereas in the latter, new pathways arise by mixing and matching of individual TS and CYP genes through dynamic genome rearrangements. This is, to our knowledge, the first documented observation of the unique pattern of TS and CYP assembly in eudicots and monocots.terpenes | terpenoid synthases | cytochrome P450 | metabolic gene clusters | genome evolution P lants produce a rich and diverse array of specialized metabolites (1, 2). These compounds have important ecological functions, providing protection against pests, diseases, UV-B damage and other environmental stresses, and serve as attractants for pollinators and seed dispersal agents. They are exploited by humans as pharmaceutics, agrochemicals, and in a wide variety of other industrial applications. Metabolic diversification in higher plants is likely to have been driven by the need to adapt and survive in different ecological niches (3, 4). Although a considerable proportion of the genes in higher plant genomes are predicted to encode enzymes with roles in metabolism (∼20% in Arabidopsis thaliana; ref. 5), most of these are as yet uncharacterized. The availability of a growing number of sequenced plant genomes now makes it possible to exploit knowledge extracted from multiple diverse species to take a more holistic approach toward understanding mechanisms of metabolic diversification in plants (1, 2).The terpenes are the largest class of plant-derived natural products, with over 40,000 structures reported to date (6-8). As such they provide an excellent entrée for investigation of mechanisms of met...