The Evolution of Functional Gene Clusters in Eukaryote Genomes

Abstract

It is increasingly clear that eukaryotic gene order is nonrandom, being constrained in some instances by expression patterns, expression levels, protein interactions or epistatic effects. The relationship between gene order and function is patchy (not every gene is in a functional cluster) and the factors that influence it are numerous and interconnected. Not surprisingly, then, our knowledge of genome structure is still growing. Here we review reported gene clusters in eukaryote genomes and obstacles such as leaky expression and tandem duplication effects for identification of functional gene clusters. In particular, we show interacting gene clusters, which are identified by protein-protein interactions (PPIs), are robust against the problems. Furthermore, we emphasize that evolutionary analyses of functional gene clusters are very important to assess their biological meaning.