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Chapter 44 : Genomic Perspectives on the Fungal Kingdom

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Abstract:

Genome sequencing has provided a means for describing the complete genetic makeup of an organism. The application of sequencing technology to fungi has provided a wealth of data of interest to medical mycologists and to evolutionary and cellular biologists alike. The sequencing of multiple fungal genomes provides an initial view of the degree of conservation and diversity within the fungal kingdom. Furthermore, the comparison of these fungal genomes with the genomes of other eukaryotes provides a more precise view both of the scale of conservation of eukaryotic genes and of novel genes restricted to the fungi. While much research on fungi has focused on understanding conserved eukaryotic functions, the genomic sequence also will be important in characterizing fungus-specific pathways such as those involved in secondary metabolism, including antibiotics, and specialized degradation pathways, such as for cellulose. The genome sequences of related organisms provide more than just catalogs of species gene content, they allow comparisons between genomes to study elements that are highly diverged and those that are highly conserved. Alignment of genes from multiple organisms, using sequence similarity search tools like BLAST or FASTA, typically identifies the most highly conserved and slowly evolving genes since they share the greatest sequence conservation. The availability of multiple genomes from a range of species with different evolutionary distances provides perspective on the evolution of gene order, content, and substitution rates. This exciting pot of data opens up new challenges and new opportunities in fungal research.

Citation: Stajich J, Dietrich F. 2006. Genomic Perspectives on the Fungal Kingdom, p 657-666. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch44

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Figure 1

Species tree of the sequenced fungi inferred from a maximum-likelihood phylogenetic reconstruction algorithm on proteins from 25 orthologous genes gleaned from whole-genome comparisons.

Citation: Stajich J, Dietrich F. 2006. Genomic Perspectives on the Fungal Kingdom, p 657-666. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch44
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Tables

Generic image for table
Table 1

List of currently funded and ongoing fungal genome sequencing projects

Citation: Stajich J, Dietrich F. 2006. Genomic Perspectives on the Fungal Kingdom, p 657-666. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch44
Generic image for table
Table 2

Top 12 most abundant fungal protein domains

Citation: Stajich J, Dietrich F. 2006. Genomic Perspectives on the Fungal Kingdom, p 657-666. In Heitman J, Filler S, Edwards, Jr. J, Mitchell A (ed), Molecular Principles of Fungal Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555815776.ch44

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