Issues in Comparative Fungal Genomics

Abstract

Biologists face an overwhelming richness of nucleotide and protein sequence data. By the middle of 2005, there were almost 300 complete genomes that were publicly accessible. Most of these were archeal or bacterial since prokaryotic genomes are much smaller than eukaryotic genomes. Among eukaryotes, fungi, particularly yeasts, have some of the smallest genome sizes and hence represent the highest number of complete or almost complete genomes sequenced. By mid-2005, there were over 43 fungal genomes that were completely or almost completely sequenced and publicly accessible. What are the relationships among fungi and between fungi and other organisms? What type of genes and pathways are required for pathogenicity and other fungal lifestyles? Researchers are addressing these types of questions with data from high-throughput genomic sequencing. This review examines some recent uses of fungal genomic data in comparative genome analyses. Comparative genomics can facilitate research into the following areas: evolution, phylogenetics, targeted drugs, gene discovery, and gene function. Each of these is discussed as well as the availability and ownership of the genomic data, and the concepts of homology (homologs, orthologs, paralogs) and similarity.

Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes

“…Results are given only as a means of providing an indication of outcomes that may be expected from such computation. For information on general analysis, the series on Fungal Genomics contains reviews on gene identification [14], comparative genomics [15], secreted proteins [16] and EST assembly [17]. The studies are from the following pathogens: the hemibiotrophic fungal pathogen Magnaporthe grisea (oryzae) that causes rice blast disease in rice; the fungal pathogen Fusarium graminearum (Gibberalla zeae) that causes head blight in wheat and barley; the biotrophic fungal pathogen Ustilago maydis that causes corn smut in maize; the two hemibiotrophic oomycete pathogens Phytophthora sojae and Phytophthora ramorum that cause root rot in soybean and sudden oak death in oak trees, respectively.…”