Comparative analysis of filamentous fungi.

James Galagan

Author address: 

Broad Institute of MIT and Harvard, Cambridge M, USA


Fungal genomes provide outstanding platforms for studying eukaryotic biology through comparative analysis. While sharing fundamental biology with other eukaryotes, their compact genomes allow comparative analysis techniques to be more easily developed and tested as compared to more complex organisms. We will describe the results of a comparative analysis of 3 related species of Aspergillus comprising a model organism (A. nidulans), a human pathogen (A. fumigatus), and an industrial agent (A. oryzae). Although members of the same genus, these species are nearly as diverged as human and fish, providing an opportunity to study genome evolution and sequence conservation over an extended evolutionary distance. We have quantified the rate of lineage-specific rearrangements in both A. oryzae and A. fumigatus. These data provide a quantitative picture of the forces driving eukaryotic genome rearrangement, and demonstrate that rates of large and small scale eukaryotic genome evolution are not always correlated. Our analysis also led to an experimentally supported model of mating-type locus evolution that suggests the potential for sexual reproduction in both A. oryzae and A. fumigatus. We identified numerous sequences actively conserved across the wide evolutionary distance separating the Aspergilli. By computationally enriching for statistical signatures correlated with function, we have identified several sequences with likely biological significance. These include two novel TPP riboswitches, and a conserved motif that suggests regulation by PUF family genes in filamentous fungi. Finally, we analyzed conserved regulatory elements called upstream open reading frames (uORFs). These are open reading frames in the 5’ UTRs of mRNAs in a wide range of species that have been shown to be able to regulate protein translation. We generated genomic and experimental evidence suggesting that uORFs play a larger role in regulating eukaryotic gene expression that has been previously suspected. Our analysis also provides the first genome-wide catalog of conserved uORFs in a eukaryote

abstract No: 

Fungal Genetics Reports (2009) Volume 56

Full conference title: 

23rd Fungal Genetics Conference
    • Fungal Genetics Conference 23rd (2002)