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FUNGAL GENETICS, MOLECULAR GENETICS, AND GENOMICS 181

used ESTs to compare the types of genes expressed by
mycelial cultures of two mycorrhizal fungi (Laccaria
bicolorand Pisolithus microcarpus) and also to compare
the genes expressed in symbiotic tissues of Pisolithus
mycorrhizas (Fig. 9.17). By comparison with EST
databases, several of the ESTs could be assigned to func-
tional groups such as genes involved in metabolism,
cell defense, or cell structure. But the majority of ESTs
showed no homology to known genes (as is also true
for whole genome sequences).
A similar EST analysis was reported by Freimoser
et al. (2003), comparing two subspecies of the common
insect-pathogenic fungus Metarhizium anisopliae– one
subspecies (M. anisopliae anisopliae) has a broad host
range and the other (M. anisopliae acridum) is a specific
grasshopper pathogen. Both strains were grown under
conditions that maximize the secretion of insect
cuticle-degrading enzymes, and a surprisingly high
proportion of ESTs could be assigned to functional
categories (Fig. 9.18). Both subspecies had ESTs for
virtually all the pathogenicity-related genes cloned to
date from M. anisopliae.

DNA microarray technology

Essentially, a DNA microarray is a small solid support
such as a microscope slide or a nylon membrane
onto which DNA is spotted (or printed by robotic
techniques) to produce hundreds or thousands of tiny
spots representing different types of DNA, arranged
in a specific order. Messenger RNAs from a sample to
be analyzed are then used to generate cDNAs, which
are fluorescently labeled so that any binding of the
cDNA to the immobilized spots on the microarray
(through complementary base-pairing) can be scanned
automatically by laser technology. There are several
types of microarray, designed for different purposes, but
the main ones usually measure one of the following:

• Changes in the level of gene expression, monitored
  automatically by mixing samples of a test DNA
  (tagged with red fluorescence) and control DNA
  (tagged with green fluorescence) so that the laser
  differentiates between the levels of expression of the
  test and control DNA.


• Changes in genomic gains and losses, again detected
  by different levels of red or green fluorescence depend-
  ing on the number of copies of a particular gene.


• Mutations in DNA, often involving only one or a few
  nucleotides.

Most of these applications are used in medicine,
including disease diagnosis, drug development and
tracking disease development, but they are equally
applicable to many aspects of basic biology and they

are becoming ever more widely used because the same

basic techniques can be done cheaply by manual spot-

ting of DNA onto solid supports. They can reveal pat-

terns of differential or coordinated expression of genes

in almost any biological system.

Online resources

Genome News Network – a quick guide to sequenced

genomes. http://w.w.w.genomesnetwork.org/

sequenced_genomes/genome_guide_p1.shtml

Microarrays: National Center for Biotechnology Infor-

mation. http://w.w.w.ncbi.nlm.nih.gov/About/primer/

microarrays.html

The Whitehead Institute, Fungal Genome Initiative.

http://www.broad.mit.edu/annotation/fungi/fgi

General texts

Bennett, J.W. & Arnold, J. (2001) Genomics for fungi. In:

The Mycota VIII. Biology of the Fungal Cell(Howard, R.J.

& Gow, N.A.R., eds), pp. 267–297. Springer-Verlag,

Berlin Heidelberg.

Bennett, J.W. & Lasure, L.L. (1991) More Gene Manipula-

tions in Fungi. Academic Press, San Diego.

Fincham, J.R.S., Day, P.R. & Radford, A. (1979) Fungal

Genetics, 4th edn. Blackwell Scientific Publishers, Oxford.

Peberdy, J.F., Caten, C.E., Ogden, J.E. & Bennett, J.W.

(1991) Applied Molecular Genetics of Fungi. Cambridge

University Press, Cambridge.

Turner, G. (1991) Strategies for cloning genes from

filamentous fungi. In: Applied Molecular Genetics of

Fungi(Peberdy, J.F., Caten, C.E., Ogden, J.E. & Bennett,

J.W., eds), pp. 29– 43. Cambridge University Press,

Cambridge.

Cited references

Anagnostakis, S.L. (1992) Diversity within populations

of fungal pathogens on perennial parts of perennial

plants. In: The Fungal Community: its organization and

role in the ecosystem(Carroll, G.C. & Wicklow, D.T., eds),

pp. 183 –192. Marcel Dekker, New York.

Bertrand, H. (1995) Senescence is coupled to induction

of an oxidative phosphorylation stress response by

mitochondrial DNA mutations inNeurospora. Canadian

Journal of Botany 73 , S198 –S204.

Buck, K.W. (1986) Fungal Virology. CRC Press, Boca Raton.

Chen, B., Choi, G.H. & Nuss, D.L. (1994) Attenuation of

fungal virulence by synthetic hypovirus transcripts.

Science 264 , 1762–1764.

Domer, J.E. & Kobayashi, G.S., eds (2004) The Mycota,

vol. XII. Human Fungal Pathogens. Springer-Verlag,

Berlin.

Edwards, S.G., O’Callaghan, J. & Dobson, A.D.W. (2002)

PCR-based detection and quantification of mycotoxigenic

fungi. Mycological Research 106 , 1005–1025.