Editorial

EDITORIAL

What is fungal genomics? Fungal genomics is the study of the structure, function, andevolution of fungal genomes. What separates this subject from traditional genetics is thestudy of 1000 or more genes or genetic markers simultaneously. As a consequence,specialized instrumentation is involved in generating genomic data, and the largeamounts of genomic information require the use of sophisticated mathematical tools forbuilding a coherent picture of a genome. These data are then made available tocommunities of scientists with novel database tools. This information has manyapplications in science, industry, agriculture, and medicine, leading to a number ofbioethical issues surrounding the uses of this public information. The new experimentaland technological approaches of genomics are thus inherently multidisciplinary,involving the contributions of individuals in molecular biology, biological instrumenta-tion, 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 artificialchromosomes (Burke et al., 1987) and novel physical mapping algorithms (Cuticchia etal., 1992), for larger eukaryotic genomes. The ability to carry out site-directedtransformation places fungi in a unique position relative to plants and animals forfunctional studies of many genes at once, the subject of functional genomics. Forexample, a library of strains containing gene knockouts is being assembled for thebudding yeast, Saccharomyces cerevisiae (Goffeau et al., 1996). In the past, only fungiwith well developed genetic tools could yield information efficiently—now genomicapproaches allow genetic information to be gleaned from even the most intractableorganisms, obligates, anaerobes, symbionts, and asexuals. The ability to use pulsed fieldelectrophoresis (Cushion et al., 1993) to separate fungal chromosomes even inunculturable mammalian pathogens, like Pneumocystis carinii, allows a single investiga-tor to create a physical map with markers evey 29 kb for such a pathogen in a singlegranting 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 varietyof fundamental biological processes, like meiosis, recombination, development, metabo-lism, virulence, and evolution. The 50 years of physiology, biochemistry, and genetics onmodel systems, like Neurospora crassa (Radford and Parrish, 1997) and Aspergillusnidulans (Clutterbuck, 1997), provide functional information on up to 10% of the genesin the genome (Kupfer et al., 1997; Radford and Parrish, 1997). The result is that fungalgenomics provides a Rosetta stone for understanding the function, biochemistry, andphysiology of the organism, on one side, and its relationship to genome structure, theunderlying genetic blueprint, on the other side.The focus of this special issue is principally on the structure of fungal genomes and the

associated experimental approaches for characterizing genome structure. Genomicstools for rapid access to previously inaccessible portions of fungal DNA for manybiological problems are illustrated in a variety of fungal systems, although genomicstudies on basidiomycetes in this issue are unfortunately absent. To understand theimpact of new experimental approaches in genetic and physical mapping and genomicsequencing, Radford and Parrish (1997) describe how traditional methods for isolating

Fungal Genetics and Biology 21, 254–257 (1997)

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genes have saturated at less than 1000 genes after 50 years of effort in one of the mostintensively studied multicellular organisms, Neurospora crassa. The upper limit hasbeen to capture only about 1⁄10 of the available genes in this system (Kupfer et al., 1997).The major impact of the Fungal Genome Initiative (Bennett, 1997) will be to unlock theremaining 9⁄10 of the genes not currently available for study, and Nelson et al. (1997)estimate ,60% of these genes will be entirely novel with no DNA sequence similaritiesto entries in GenBank, such as the DNA sequence of S. cerevisiae (Nature 387,supplement, May 29, 1997). The availability of tools like AFLP maps (Van der Loo et al.,1997) and physical maps (Xiong et al., 1996; Rosa et al., 1997; Schmidhauser et al., 1997;Tait et al., 1997; Wan et al., 1997; Zhu et al., 1997) is leading to an estimated threefoldincrease in the rate at which genes can be isolated (Balding and Torney, 1997). Forexample, it has taken approximately 17 years to clone on the order of ,60 genes in A.nidulans, but in the last 2 years the number of available genes on the physical map in A.nidulans (Xiong et al., 1996; http://fungus.genetics.uga.edu:5080) has approximatelydoubled.Aleksenko and Clutterbuck (1997) in one of the few functional studies review how

eukaryotic extrachromosomal plasmids are providing a doorway to understandingchromosomal origins (e.g., yeast ARS sequences) for replication, how they enhancerecombination and uptake of exogenous DNA, and how they amplify DNA in fungi. Twofunctional classes of DNA sequences, which support the extrachromosomal replicationof bacterial plasmids, are described. One class contains DNA sequences (i.e., AMA1elements) that promote effective plasmid replication. The other class contains DNAsequences (i.e., MATE elements) that enhance transformation efficiency. In some casesboth classes of elements are found in close proximity on a chromosome. The fungaltransformation enhancers may then be linked to other processes in fungal genomes, suchas replication, recombination, and DNA amplification.One technology that will play a critical role in understanding genomic function is

monitoring the simultaneous expression of many genes by microarraying cDNAs(Schena et al., 1995; Shoemaker et al., 1996) under two conditions of some biologicalprocess, like development or virulence. Total RNA from strains with and withoutconidiation (or avirulence) might be labeled with red and green fluorescent dyes,reverse-transcribed, and then used to wash cDNAs microarrayed and immobilized on alysine-coated microscope slide. Differential expression between the two RNA sources isthen used to identify genes that may be involved in the process. A library of site-directedknockouts could then be generated from this candidate list of genes impacting theprocess and used for new RNA sources for microarraying to determine what genes fallupstream or downstream in relevant pathways.Another related functional genomics tool is negative genetic selection (Hensel et al.,

1995). Cosmids in a library can be equipped with sequence-tagged sites (STSs) anduniversal primers for polymerase chain reaction (PCR), and a knockout library can becreated coupled to methods, like the microarray technology. Pools of clones can then betransformed into fungi, and two conditions of some process can be scored on pools oftransformants. DNA recovered by PCR under two conditions relevant to the processbeing studied, i.e., conidiation (avirulence) vs no conidiation (virulence) can behybridized to the gene knockout library arrayed on nylon membranes. Differentialrecovery of the STSs under these two conditions allows inferences about what cosmids(and the genes they contain) are involved in the process. The efficiency of this negativeselection is increased threefold by the availability of a physical map (Balding and Torney,1997) in the case of A. nidulans.

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What is unique about fungi is the ability to examine genome evolution experimentallyand the underlying process with pulsed field electrophesis and rapid physical mappingtechniques. More recent studies of chromosome evolution have focused on descriptiveaspects of chromosome evolution, the synteny between mammalian (O’Brien et al.,1993) and plant genomes (Ahn et al., 1993). The first substantial example of synteny inthe ‘‘Fifth Kingdom’’ is between the cotton pathogen, Ashbya gossypii, genome and S.cerevisiae genome (Altmann-Johl and Phillippsen, 1996). This kind of chromosomalsimilarity between related species is an important example of what is likely to be anincreasingly important avenue by which model systems in fact aid in the study of lesstractable relatives, such as cloning by synteny of homologous genes (Agnan et al., 1997).As genomic sequence continues to accumulate on fungal genes, this information also

becomes useful in functional studies of genes. Todd and Andrianopoulous (1997) createa phenogram for 80 proteins with a zinc finger motif found exclusively in fungaltranscriptional regulators. Within this phenogram there are certain subclasses oftranscriptional regulators that have shared functions. The phenogram provides apredictor of function for novel zinc finger proteins.The experimental approaches available only in fungi at the moment will allow

evolutionary biologists to examine in detail the tempo and mode of chromosomalevolution with much the same ease as the large effort devoted to the molecular evolutionof individual genes in other eukaryotic systems. Fungi are likely to provide fundamen-tally new insights into the genome evolution of eukaryotes.Some of the shift to functional and evolutionary studies of fungal genomes and a

broader array of structural studies of fungal genomes are likely to be reflected at the 2ndFungal Genome Workshop, March 27–28, 1998, at Georgia Center for ContinuingEducation, University of Georgia, Athens, Georgia 30602.

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