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Chapter 40 : Studying Fungal Virulence by Using Genomics

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Abstract:

This chapter makes evident, genomics, in particular genomic microarrays, hold great promise for mycological research. To this end, the chapter covers the current state of fungal genome sequencing and the advantages of and obstacles to using this emerging data for genomic projects, the "pregenomic" methods used for finding in vivo-expressed genes and how these efforts provide intellectual support for expression profiling studies, and a discussion of options for microarray development. It reviews a few selected microarray-based studies directly relevant to fungal pathogenesis. The process by which chromosome III and the rest of the genome was sequenced produced extremely high-quality sequence data, in terms of both accuracy and completeness. Like differential display, serial analysis of gene expression (SAGE) is a simple idea backed by complicated molecular biology. Indeed, in the SAGE study of from rabbit cerebrospinal fluid 35% of the tags found only in vivo are orphans. Microarray analysis of phagocytosed cells identified 36% of upregulated genes as unique to this species, roughly twice what would have been expected if the distribution was random. Genomics, along with proteomics, large-scale and signature-tagged mutagenesis, and sequencing efforts, have added powerful new approaches to our repertoire. Although most of these have not been fully utilized to date, the incorporation of these technologies into mycological studies will allow unprecedented progress in understanding the biology and pathology of these fascinating and important organisms.

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40

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Figures

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Figure 1

Schematics for array experiments. (A) All samples are compared to the precursor ( = 0) sample. (B) All samples are compared to time-matched controls. (C) Reference sample design in which all samples are compared to a constant RNA population. See the text for a description of the merits of each design.

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40
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Figure 2

Microarray analysis of pheromone response pathway components. The induction of each gene is indicated after treatment with 50 nM α-factor for 30 min. Data from reference .

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40
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Tables

Generic image for table
Table 1

Published fungal genome sequences

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40
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Table 2

Selected unpublished fungal sequences of medical or agricultural importance

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40
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Table 3

Comparison of expression-based approaches

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40
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Table 4

Relevant features of microarray types

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40
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Table 5

Top 20 genes induced by α-factor in microarray experiments

Citation: Lorenz M. 2006. Studying Fungal Virulence by Using Genomics, p 591-609. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch40

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