Editorial

Abstract

What is fungal genomics? Fungal genomics is the study of the structure, function, and evolution of fungal genomes. What separates this subject from traditional genetics is the study of 1000 or more genes or genetic markers simultaneously. As a consequence, specialized instrumentation is involved in generating genomic data, and the large amounts of genomic information require the use of sophisticated mathematical tools for building a coherent picture of a genome. These data are then made available to communities of scientists with novel database tools. This information has many applications in science, industry, agriculture, and medicine, leading to a number of bioethical issues surrounding the uses of this public information. The new experimental and technological approaches of genomics are thus inherently multidisciplinary, involving the contributions of individuals in molecular biology, biological instrumentation, computational biology, databases, statistics, and bioethics.Fungi have played a key role in the development of genomics. Their compact genomes have been exploited to develop new genomic tools, like yeast artificial chromosomes (Burke et al., 1987) and novel physical mapping algorithms (Cuticchia et al., 1992), for larger eukaryotic genomes. The ability to carry out site-directed transformation places fungi in a unique position relative to plants and animals for functional studies of many genes at once, the subject of functional genomics. For example, a library of strains containing gene knockouts is being assembled for the budding yeast, Saccharomyces cerevisiae (Goffeau et al., 1996). In the past, only fungi with well developed genetic tools could yield information efficiently-now genomic approaches allow genetic information to be gleaned from even the most intractable organisms, obligates, anaerobes, symbionts, and asexuals. The ability to use pulsed field electrophoresis (Cushion et al., 1993) to separate fungal chromosomes even in unculturable mammalian pathogens, like Pneumocystis carinii, allows a single investigator to create a physical map with markers evey 29 kb for such a pathogen in a single granting cycle, thereby converting an intractable system into a ''model system.'' Fungal genetics is entering a renaissance because it is now feasible to study simultaneous expression of all genes in a fungal genome (Schena et al., 1995) in a variety of fundamental biological processes, like meiosis, recombination, development, metabolism, virulence, and evolution. The 50 years of physiology, biochemistry, and genetics on model systems, like Neurospora crassa (Radford and Parrish, 1997) and Aspergillus nidulans , provide functional information on up to 10% of the genes in the genome (Kupfer et al., 1997; Radford and Parrish, 1997). The result is that fungal genomics provides a Rosetta stone for understanding the function, biochemistry, and physiology of the organism, on one side, and its relationship to genome structure, the underlying genetic blueprint, on the other side.The focus of this special iss...

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