My initial work with the M. grisea and N. crassa genomes reveals that many segments of conserved synteny (groups of orthologous genes that are found in close proximity to one another) can be found between the two species despite more than 200 million years of divergent evolution. This provides us with the opportunity to study events such as genome rearrangements in an effort to understand what role they have in the evolution of plant pathogenic fungi. Additionally, segments of conserved synteny among closely related fungi could be used to aide in genome annotation, since this information can provide clues about the location and function of genes in unannotated genomes. As our knowledge of the structure of fungal genomes grows, there are an increasing number of examples of genes belonging to common metabolic pathways that also are also found in close proximity to one another in the genome. These gene clusters are usually rare, and thought to be species specific. However, in some cases, gene clusters can be found in evolutionarily divergent species, suggesting that there is a functional constraint to genome rearrangement in the cluster. One prominent example is the quinic acid gene cluster (Qa cluster), a cluster of 7 genes that have related function and gene expression patterns. All 7 genes in this cluster are found in clusters in the genomes of M. grisea, N. crassa, F. graminearum, and A. nidulans, species separated by more than 200 million years of evolution. The genes in this cluster are adjacent to each other in all four fungi though the relative order of the genes is not maintained between species. A second example is the MAT locus, which contains genes required for mating type recognition. By identifying other conserved gene clusters, we will be able to understand the functional constraints that limit genome reorganization, and their role in genome evolution.
- C-Hunter: An algorithm for finding clusters of functionally related genes in genomes.