In bacteria, genes with related functions often are grouped together in operons and are cotranscribed as a single polycistronic mRNA. In eukaryotes, functionally related genes generally are scattered across the genome. Notable exceptions include gene clusters for catabolic pathways in yeast, synthesis of secondary metabolites in filamentous fungi, and the major histocompatibility complex in animals. Until quite recently it was thought that gene clusters in plants were restricted to tandem duplicates (for example, arrays of leucine-rich repeat disease-resistance genes). However, operon-like clusters of coregulated nonhomologous genes are an emerging theme in plant biology, where they may be involved in the synthesis of certain defense compounds. These clusters are unlikely to have arisen by horizontal gene transfer, and the mechanisms behind their formation are poorly understood. Previously in thale cress (Arabidopsis thaliana) we identified an operon-like gene cluster that is required for the synthesis and modification of the triterpene thalianol. Here we characterize a second operon-like triterpene cluster (the marneral cluster) from A. thaliana, compare the features of these two clusters, and investigate the evolutionary events that have led to cluster formation. We conclude that common mechanisms are likely to underlie the assembly and control of operon-like gene clusters in plants.O perons are a familiar feature of prokaryote genomes, where genes belonging to the same functional pathway are assembled into a single transcriptional unit. In eukaryotes, operons are rare [with a few notable exceptions such as in the genomes of nematodes (1)], and functionally related genes usually are scattered across the genome. However, eukaryotic gene order is not as random as it first appeared, and clusters of functionally related but nonhomologous genes now have been identified in the genomes of animals and fungi (2, 3). These clusters include the MHC locus in mammals (4), gene clusters for nutrient use in yeast (5-7), and numerous clusters for diverse secondary metabolic pathways in filamentous fungi (8,9). Although the genes within these eukaryotic clusters are transcribed independently, these clusters have certain operon-like features (physical clustering and coregulation) (3).In plants, genes for well-characterized secondary metabolic pathways such as the anthocyanin pathway are unlinked. However, the first gene cluster for a plant secondary metabolic pathway-for the synthesis of cyclic hydroxamic acids-was discovered in maize (Zea mays) in 1997 (10), and since then a secondary metabolic gene cluster for the synthesis of the triterpene avenacin has been discovered in diploid oat (Avena strigosa) (11-14), and two clusters for the synthesis of different diterpenes (momilactones and phytocassanes) have been characterized in rice (Oryza sativa) (15-18). These four clusters from cereals are all required for the synthesis of preformed or stress-induced compounds implicated in plant defense (15,16,19,20). We recently identifie...