Patterns of genome evolution across the fungal kingdom

A comparative genomics analysis of over 200 fungal genomes has revealed large differences in genome evolution across the fungal kingdom. These differences are caused by variable rates of interchromosomal rearrangements, variable inversion lengths in intrachromosomal rearrangements, and variable rates of tandem duplications. Each class of fungi follows its own pattern of genome evolution. An important driving force behind these diffences are repetitive elements. Moreover, these various patterns of genome evolution have important implications for gene localization.

For example, it was previously shown in the class Dothideomycetes (phylum Ascomycota) that a low rate of interchromosomal rearrangements and high rate of intrachromosomal rearrangements leads to mesosynteny, where gene content but not gene order is conserved. In the class Saccharomycetes (phyum Ascomycota), in contrast, interchromosomal rearrangements occur frequently, quickly degrading conserved syntheny. A similar pattern of genome evolution as in Dothideomycetes occurs in the class Agaricomycetes (phylum Basidiomycota), with the important difference that the intrachromosomal inversion length is much smaller. This results in a distinct pattern only found in this class. Moreover, in Agaricomycetes several conserved ancestral chromosomes could be identified with varying patterns of genome evolution, likely due to their difference in sequence composition.

On gene level, conserved gene clusters were identified despite the observed intrachromosomal inversions. Notably, certain transcription factors were over-represented in these conserved gene clusters.