A comparative genomic investigation of fungal genome evolution

High throughput genome sequencing has enabled the study of entire organism's genomes without knowing the functions of the individual genes. Comparative genomics provides a tool for studying how genomes evolve. The availability of genome sequences for several dozens of species makes it possible to pose questions about the origin of the complex genomes of eukaryotes. I performed analyses of gene structure and gene family evolution after developing automated methodologies to annotate fungal genomes and identify orthologous and paralogous genes.; The exon-intron gene structures of fungi vary in intron density from less than one to over six per gene. I evaluated the gene structure of orthologous genes across the fungal kingdom to test whether fungal intron positions represent ancestral states or recent acquisitions. This work found that intron positions are shared among the plants, animals, and fungi indicating many introns were at least present in the common eukaryotic crown group ancestor. The intron-poor hemiascomycete yeast species were shown to have lost introns recently rather than introns having been gained independently in the basidiomycete and euascomycete lineages. This work confirms previous results that used intron-poor species as fungal representatives of the kingdom but increases the number of intron positions in the fungal-animal ancestor to more than 4.5 per kilobase of protein coding gene sequence.; I compared the exon-intron structures of genes from the genomes of closely related species of the fungus Cryptococcus neoformans to identify recent examples of intron loss and gain. This analysis found several genes with adjacent introns indicating intron loss via homologous recombination with a cDNA. Few examples of intron gain were found, suggesting that intron loss is the major driving force in exon-intron structure change among these closely related species.