The rise of operon-like gene clusters in plants

• Gene clusters in plants encode secondary metabolites implicated in defense.
• Clustering of entire pathways facilitates co-inheritance and co-regulation.
• Cluster prediction and regulation studies require a multidisciplinary approach.
• Cluster knowledge can serve crop biofortification and industrial production.

Gene clusters are common features of prokaryotic genomes also present in eukaryotes. Most clustered genes known are involved in the biosynthesis of secondary metabolites. Although horizontal gene transfer is a primary source of prokaryotic gene cluster (operon) formation and has been reported to occur in eukaryotes, the predominant source of cluster formation in eukaryotes appears to arise de novo or through gene duplication followed by neo- and sub-functionalization or translocation. Here we aim to provide an overview of the current knowledge and open questions related to plant gene cluster functioning, assembly, and regulation. We also present potential research approaches and point out the benefits of a better understanding of gene clusters in plants for both fundamental and applied plant science.