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Recent progress, developments, and issues in comparative fungal genomics

Biologists face an overwhelming richness of nucleotide and protein sequence data. As of the end of 2003, there were over 100 complete or almost complete nonviral genomes in publicly available databases. Most of these were bacterial, since prokaryotic genomes are generally much smaller in size than eukaryotic genomes. Among eukaryotes, fungi have some of the smallest genome sizes and, hence, represent the highest number of complete or almost complete genomes sequenced, with most of these released within the last 2 years. What are the genes that fungi have in common? Among these genes, which ones have homologs in plants, animals, or bacteria, and which ones are only found in fungi? Researchers are just beginning to be able to address these types of questions with data from high-throughput genomic sequencing. This paper examines some recent and possible future uses of fungal genomic data in comparative genome analyses, particularly as they relate to the study of fungal plant pathogens. Comparative genomics can facilitate research into the following areas: phylogenetics (via whole genome comparisons), targeted drugs (via unique target sites in pests), gene discovery (via conserved sequences), and gene function (via guilt by association). Each of these is discussed as well as the availability and ownership of the genomic data, and the concepts of homology and similarity.