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...

Transposable elements (TEs) are the primary contributors to the genome bulk in many organisms and are major players in genome evolution. A clear and thorough understanding of the population dynamics of TEs is therefore essential for full comprehension of the eukaryotic genome evolution and function. Although TEs in Drosophila melanogaster have received much attention, population dynamics of most TE families in this species remains entirely unexplored. It is not clear whether the same population processes can account for the population behaviors of all TEs in Drosophila or whether, as has been suggested previously, different orders behave according to very different rules. In this work, we analyzed population frequencies for a large number of individual TEs (755 TEs) in five North American and one sub-Saharan African D. melanogaster populations (75 strains in total). These TEs have been annotated in the reference D. melanogaster euchromatic genome and have been sampled from all three major orders (non-LTR, LTR, and TIR) and from all families with more than 20 TE copies (55 families in total). We find strong evidence that TEs in Drosophila across all orders and families are subject to purifying selection at the level of ectopic recombination. We showed that strength of this selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs in the same family. Importantly, these rules do not appear to vary across orders. Finally, we built a statistical model that considered only individual TE-level (such as the TE length) and family-level properties (such as the copy number) and were able to explain more than 40% of the variation in TE frequencies in D. melanogaster.

Studies of the population dynamics of transposable elements (TEs) in Drosophila melanogaster indicate that consistent forces are affecting TEs independently of their modes of transposition and regulation. New sequencing technologies enable biologists to sample genomes at an unprecedented scale in order to quantify genome-wide polymorphism for annotated and novel TE insertions. In this review, we first present new insights gleaned from high-throughput data for population genomics studies of D. melanogaster. We then consider the latest population genomics models for TE evolution and present examples of functional evidence revealed by genome-wide studies of TE population dynamics in D. melanogaster. Although most of the TE insertions are deleterious or neutral, some TE insertions increase the fitness of the individual that carries them and play a role in genome adaptation.