The first gene cluster for a secondary metabolic pathway was discovered in maize ( Zea mays ) over a decade ago ( Frey et al., 1997 ) and was regarded as something of an oddity. However clusters of genes for secondary metabolic pathways are now an emerging theme in plant biology, and are providing some provocative insights into plant genome plasticity and evolution. Gene clusters containing nonhomologous functionally related genes are common in bacterial genomes. Most are organized as operons, in which the different genes are expressed as a single polycistronic mRNA allowing the tight coupling of transcription and translation ( Zheng et al., 2002 ; Rocha, 2008 ; Koonin, 2009 ). Operons, in turn, may be clustered. For example in actinomycetes, which produce a prolific array of pharmaceuticals and other high-value molecules, the genes for secondary metabolite production are clustered and typically encode several transcripts, some of which are bi- or polycistronic ( Osbourn, 2010 ). True operons are rare in eukaryotes because transcription is uncoupled from translation and mRNAs are generally monocistronic; therefore, genes under common regulation are often dispersed throughout the genome and coordinately regulated in trans. Although there are clusters of functionally related genes
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