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FUNGAL BIOLOGY
A Textbook by JIM DEACON
Blackwell Publishing 2005

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CHAPTER 9: FUNGAL GENETICS, MOLECULAR GENETICS AND GENOMICS

Chapter 9 is divided into the following major sections:

overview: the place of fungi in genetical research
Neurospora and classical (Mendelian) genetics
structure and organisation of the fungal genome
genetic variation in fungi
applied molecular genetics of fungi
Returning to the genome
expressed sequence tags and microarray technology

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In this chapter we cover the basic and applied genetics of fungi, including the features that continue to make fungi important model organisms for genetical research. The chapter includes recent molecular approaches in a range of fields such as the analysis of fungal pathogenicity determinants and the development of fungi as ‘factories’ for foreign gene products. It also covers the roles of extrachromosomal genes in ageing-related senescence and the effects of fungal viruses (hypoviruses) in suppressing pathogenic virulence.

Fungi are eminently suitable for biochemical studies because of their simple nutrient requirements, and because ‘classical genetics’ has provided excellent physical maps of the chromosomal genes. Studies on one fungus in particular – Neurospora crassa – led to the classical concept of ‘one gene, one enzyme’, for which Beadle & Tatum (1945) received the Nobel Prize. However, with more recent knowledge it is more accurate to say that ‘one gene can encode one enzyme’ – the situation is complicated because gene splicing occurs to remove non-coding introns in the pre-messenger RNA.

At the time of writing (May 2004), the genomes of nearly 150 organisms have been sequenced – mainly bacteria and archaea, but also the genomes of mouse and ‘man’. Notably in our present context, the ‘high-quality draft’ genome sequences of five fungi have been published – Saccharomyces cerevisiae, Neurospora crassa, Emericella (Aspergillus) nidulans, Schizosaccharomyces pombe and the rice blast pathogen, Magnaporthe grisea. The first four of these are Ascomycota with well-mapped chromosomes, providing a basis for combining classical and molecular genetics.

Chapter 9 images. Click on thumbnails

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[see text for
Figs 9.17 and 9.18]

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Table 9.1. Reported chromosome counts in some representative fungi
Oomycota  
Phytophthora spp. (many)   9-10
Achlya spp. 3, 6, 8
Saprolegnia spp. 8-12
Pythium commonly 10 or 20
Chytridiomycota  
Allomyces arbuscula 16
A. javanicus 14 (variable in hybrids and polyploids)
Ascomycota  
Schizosaccharomyces pombe 3
Neurospora crassa 7
Saccharomyces cerevisiae 16
Emericella (Aspergillus) nidulans 8
Coccidioides posadasii 4
Trichophyton rubrum 4
Magnaporthe grisea 7
Basidiomycota  
Filobasidiella neoformans 11
Schizophyllum commune 11
Coprinus cinereus 13
Puccinia kraussianna 30-40

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Table 9.2. Some reported (approximate) genome sizes of fungi and fungus-like organisms
Aspergillus fumigatus (potential human pathogen) 30 Mb
A. niger (industrially important: citric acid, enzyme production) 30 Mb
Candida albicans (human commensal and potential pathogen) 16 Mb
Filobasidiella (Cryptococcus) neoformans (human pathogen) 21 Mb
Emericella (Aspergillus) nidulans (experimental model fungus) 28 Mb
Neurospora crassa (experimental model fungus) 40 Mb
Phanaerochaete chrysosporium (wood-decay Basidiomycota) 40 Mb
Phytophthora infestans (plant pathogen; Oomycota) 240 Mb
Phytophthora sojae (pathogen of soybean; Oomycota) 62 Mb
Pneumocystis jiroveci (pathogen of immunocompromised humans) 7.7 Mb
Saccharomyces cerevisiae (brewing and breadmaking yeast) 12 Mb
Schizosaccharomyces pombe (experimental model; fission yeast) 14 Mb

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Table 9.4. A list of fungi initially proposed to form the basis of a co-ordinated genome sequencing effort in the USA
Organisms bycategory Significance (and chapter reference)
[See footnotes to this table]
Estimated genome (Mb)
MEDICINE  
Filobasidiella (Cryptococcus) neoformans serotype A Basidiomycota. Encapsulated yeast; causes fatal meningitis in humans 24 Mb on 11 chromosomes
Coccidioides posadasii Ascomycota. Soil fungus endemic to southwestern USA; causes fatal human infection; also a bioterrorism threat 29 Mb on 4 chromosomes
Pneumocystis carinii (human and mouse forms) The leading opportunistic pathogen of AIDS patients; drug resistance is emerging 7.5; 6.5 Mb
Trichophyton rubrum Ascomycota. The most common fungal infection in the world; adapted for growth on human skin 12 Mb on 4 chromosomes
Rhizopus oryzae Zygomycota. Can cause infection of humans (zygomycosis) 36 Mb
COMMERCE  
Magnaporthe grisea Causes rice blast disease. A model fungal plant pathogen 40 Mb on 7 chromosomes
Aspergillus flavus Ascomycota/ mitosporic fungus. Source of aflatoxin and one cause of human aspergillosis 40 Mb on 8 chromosomes
Emericella (Aspergillus) nidulans Ascomycota. Key model system for genetics and cell biology. (Already part-sequenced) 31 Mb on 8 chromosomes
Aspergillus terreus Mitosporic fungus. Major source of the cholesterol-lowering drug, lovastatin 30 Mb
Fusarium graminearum Mitosporic fungus. Causes head blight on wheat and barley; produces mycotoxins. 40 Mb on 9 chromosomes
EVOLUTION/ FUNGAL DIVERSITY  
Neurospora discreta Ascomycota. Fungal model for population genetics and comparison with N. crassa (already sequenced) 40 Mb on 7 chromosomes
Coprinus cinereus Basidiomycota. Model for fungal differentiation – produces toadstools 37.5 Mb on 13 chromosomes
Batrachochytridium dendrobatidis Chytridiomycota. Recently described fungus that causes widespread population decline of amphibians 30 Mb on 20 (?) chromosomes
Ustilago maydis Basidiomycota. Model for plant-pathogen interactions 20 Mb
Paxillus involutus Basidiomycota. Symbiotic mycorrhizal fungus of many trees, easily manipulated in laboratory conditions 40 Mb

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