Introduction to the special issue of the Revista Iberoamericana de Micología devoted to Fungal Genomes

Abstract

Since the first genome sequence for a free-living organism, Haemophilusinfluenzae, was published in 1995 [6], 36 fungal sequencing projects have beenstarted. At present, nine have been completed, 22 are at Whole GenomeShotgun assembly and five are in progress [1]. The complete sequencing of thegenome of the baker’s yeast, Saccharomyces cerevisiae, the first fungal genomesequenced [5], is considered a landmark in Genomics [3] and the deciphering ofthe fungal genome represents a unique opportunity to enhance the knowledgewe have on those organisms as well as opens the door to benefits that wereprophesied to include “magic bullet” therapeutics, individualized medicine, andthe prediction of disease long before symptoms surface. However, these bre-akthroughs are not straightforward and we must realize that we must fashion thefour-letter code we all share into tools physicians can use, and ensure that thesetools are readily available [2].In this issue of the Revista Iberoamericana de Micologia devoted to FungalGenomes there are a number of papers in which scientists involved in sequen-cing projects review the impact of the knowledge of the genome of each fungushas or will have on a variety of basic and applied aspects.The impact of a completed fungal genome sequence on the development ofnovel therapeutics for human disease may occur in three areas: improvedunderstanding of disease causation at the molecular level, improved diagnosisand disease classification based on genetic profiles, and new therapeutics basedon targets identified in the genome. These improvements will require increasedphysician understanding of genetic principles applied to common diseases.The current increase in the number of microbes resistant to antibacterial or anti-fungal agents represents a potential crisis in human and veterinary medicine.Some believe that we are entering a post-antibiotic era where most antibiotics nolonger will be efficacious [4]. Therefore, it is important that new antibiotics bedeveloped. However, because of the potential for cross-resistance, new targetsfor the discovery of antibiotics are needed particularly where resistance does notcurrently exist. The results obtained from the sequencing of genomes from pa-thogenic fungal microbes provide an opportunity to ameliorate this problem.Genomic sequence data can be used to identify new genes that could be usedas targets for new antifungal discoveries. Viable new target genes might repre-sent those that are widely distributed among fungal pathogens or that havehomologs and are essential for the viability of the organism. Novel, non-traditio-nal targets also will be found through the analysis of genome sequences: thosethat are involved in disease pathogenesis and those that are involved in adapta-tion and growth in infection sites. The advantage of the non-classical targets isthat targeting these sites may not result in the same degree of selective pressurethat encourages resistance, and these could have a longer therapeutic life time.The usefulness of the comparative analyses of fungal genomes and molecularresearch on the discovery of fungal genes associated with putative targets fornovel antifungal agents is reviewed in one of the papers of this issue.The fungal research community has enthusiastically embraced the utilization ofgenomics technologies to resolve long-standing issues in fungal biology. Forexample, such technologies have been proposed to study the mechanics of tipgrowth, photoreception, gene silencing, the molecular basis of conidiation, thepathway leading to sexual reproduction, and mechanisms of pathogenesis [7].The resulting databases will allow the comprehensive analysis of developmentalprocesses that are characteristic of fungi, including the molecular nature of pa-thogenicity. DNA databases underpin analyses of the fungal transcriptome, pro-teome, and metabolome. This combined information will contribute to our basicunderstanding of not only the mechanics of infection but also the evolution ofpathogenicity. The application of genomic approaches such as comparativegenomics to identify sequences that contribute to infection and disease and func-tional genomics and proteomics to analyze global patterns of gene and proteinexpression involved in fungal pathogenesis and diagnosis are reviewed in one ofthe papers of this issue.