513 Complete and partial genome sequence information is underway in several parasitic and symbiotic fungi that infect humans, other animals and plants. Comparative analyses of these sequences will provide new insights into the genomic plasticity and evolution of parasitism and mutualism in fungi. Addresses *Department of Microbial Ecology, Lund University, Ecology Building, SE-223 62 Lund, Sweden; e-mail: anders.tunlid@mbioekol.lu.se † School of Biological Sciences, University of Exeter, Washington Singer Laboratories, Perry Road, Exeter, EX4 4QG, UK; e-mail: N.J.Talbot@exeter.ac.uk Current Opinion in Microbiology 2002, 5:513–519 1369-5274/02/$ — see front matter © 2002 Elsevier Science Ltd. All rights reserved. Published online 9 September 2002 Abbreviations AM arbuscular mycorrhiza BAC bacterial artificial chromosome EST expressed sequence tag HGT horizontal gene transfer mC methylated cytosine Introduction Approximately 100,000 species of fungi have been described so far, and approximately 10% of these obtain nutrients by living in close association with other organisms, such as plants and animals, including humans. Many fungal infections are parasitic and can lead to severe diseases. Other infections are mutualistic symbioses that are beneficial to the host organism. This group includes infections caused by the mycorrhizal fungi that infect the roots of many important crops and forest trees. These fungi improve the growth of the host plants by facilitating the uptake of nutrients such as nitrogen and phosphate from the soil. Our understanding of how parasitic and symbiotic fungi infect their hosts, including the mechanisms of host recognition, development of infection structures, control of host defense reactions, and penetration and colonization of the host tissues, is limited. However, it can be expected that this situation will change rapidly in the coming years, because a large amount of information from the genome sequences of fungal pathogens and symbionts will shortly become available. Over the past five years, a corresponding flow of information about prokary- otes has had a major impact on the research of bacterial pathogenesis and symbiosis [1,2]. Comparative genomics of strains and species of bacteria has also provided new insights into the evolution of virulence and host adaptations. The con- current development of post-genomic methods to determine gene function has transformed research into bacteria–host interactions from a piecemeal study of individual genes and proteins to a more systematic analysis of the entire gene and protein complements of microbial pathogens. Since completion of the Saccharomyces cerevisiae genome in 1996 [3], progress on the sequencing of other fungal genomes has been limited. However, early this year, the annotated genome of the fission yeast Schizosaccharomyces pombe was published [4], and genome sequencing of several fungal species is nearing completion. These species include the filamentous fungus Neurospora crassa (http://www-genome.wi.mit.edu/annotation/fungi/ neurospora/), the human pathogens Candida albicans and Cryptococcus neoformans, and the phytopathogen Magnaporthe grisea (the causal agent of rice blast). Genome sequence information and expressed sequence tag (EST) collections from several other parasitic and symbiotic fungi that infect humans, other animals and plants are also becoming more widespread (Table 1). In this review, we discuss the recent achievements in fungal genomic analyses and how such data can provide new insights into genomic plasticity and the evolution of parasitic and mutualistic life styles. Genome diversity of parasitic and symbiotic fungi Compared with the genome sizes of other eukaryotes such as animals and plants, the genome sizes of fungi are small. S. cerevisiae and S. pombe have genome sizes of 13.7 Mb and 13.8 Mb, respectively [3,4]. Except for the filamentous ascomycete Ashbya gossypii, which has a genome size of 8.9 Mb, other filamentous ascomycetes and basidio- mycetes have genome sizes between 13–42 Mb [5,6]. Thus, the genome sizes of fungi are approximately one- third of those of Caenorhabditis elegans and Arabidopsis thaliana, and are an order of magnitude smaller than the genome of rice (Oryza sativa). Furthermore, fungal genomes have a high gene density, and a low proportion of repetitive sequences. For example, S. cerevisiae contains a gene approximately every 2 kb [3], whereas the larger genome of N. crassa contains a gene every 4 kb (http://www-genome.wi.edu/annotation/fungi/neurospora). The gene density in M. grisiae is estimated to be approximately one gene every 4.2 kb [7], and for the ectomycorrhizal fungus Paxillus involutus, one gene every 2.8 kb [8]. The genomes of the arbuscular mycorrhizal (AM) fungi have unusual sizes and structures. AM fungi are obligate symbionts and are all found in the order Glomales. The genome sizes of these fungi have been estimated to be 100–1000 Mb, which is significantly larger than those of ascomycetes and basidiomycetes [9]. The GC (guanine and cytosine) content of AM fungi is also significantly lower (30–35%) than the range of 40–56% reported for other fungi [6,10]. Compared with other fungi, the genomes of glomalean fungi have a higher proportion of methylated cytosine (mC), a fact that offers some explana- tion for the evolution of the large, adenine and thymine (AT)-rich genomes of AM fungi [9,10]. Mutation of mC Genomics of parasitic and symbiotic fungi Anders Tunlid* and Nicholas J Talbot †