untitled

gene copy is free to mutate and can eventually assume
a new function while the original gene retains its
function. But this process is blocked in Neurospora
during the haploid dikaryotic phase of the sexual
cycle (Chapter 2). The RIP process detects and mutates
both copies of a duplicated gene by causing numerous
mutations from G-C to A-T pairs, and often leads to
DNA methylation which causes gene silencing in
Neurospora(as DNA methylation also does in mammals).
The effects of this can extend to adjacent genes
beyond the duplicated sequences. Consistent with this
role of RIP, N. crassahas an unusually low proportion
of genes in mutigene families, in relation to its
genome size, and it has almost no highly similar gene
pairs. Several other lines of evidence support the view
that genome evolution in N. crassahas been largely

arrested since the acquisition of RIP at some point in

its evolutionary history.

It is suggested that RIP acts as a defense against

“selfish DNA,” thereby protecting the genome. Con-

sistent with this is the fact that no intact mobile

elements were detected in the genome sequence,

and 46% of repetitive nucleotides can be identified

as relics of mobile elements. Sequence comparisons

with other Neurosporaspp. would help to address the

broader significance of these findings.

Even though N. crassahas an impressive array of

genome defense mechanisms, it is not unique in

having defense systems. For example, the many anas-

tomosis groups and vegetative compatibility loci in

Rhizoctonia solaniand Cryphonectria parasiticaprobably

serve similar functions in impeding the spread of

potentially damaging mobile viruses or other genetic

elements.

FUNGAL GENETICS, MOLECULAR GENETICS, AND GENOMICS 179

Table 9.5Neurospora crassagenome features. (From

Galagan et al. 2003.)

Feature Measurement

Size (base pairs) 38,639,769

Chromosomes 7

Protein-coding genes 10,082

Transfer RNA genes 424

5S rRNA genes 74

Per cent coding 44

Per cent introns 6

Average gene size (base pairs) 1673 (481

amino acids)

Average intergenic distance (base pairs) 1953

Predicted protein-coding sequences:

Identified by similarity to known 13%

sequences

Conserved hypothetical proteins 46%

Predicted proteins (no similarity 41%

to known sequences)

A C U G

Ribonuclease digestion of RNA

Synthesis of second strand of DNA

mRNA

RNA

Reverse

transcriptase

cDNA

Double

stranded

DNA

Reverse sequencing primer

Forward sequencing primer

3 ′ EST

A C U G

T G A C

A C T G

T G A C

5 ′ EST

Fig. 9.16Procedure for generating cDNA from messen-

ger RNA, then producing expressed sequence tags (ESTs)

from either the 5′or 3′end of cDNA.

Table 9.4(cont’)

(^8) Fusarium graminearum. Produces several mycotoxins and represents a major genus of food-spoilage organisms.
(^9) Neurospora discreta. Would enable comparisons with N. crassa (a fungus that used to be a serious contaminant of bread, but
nowadays is rare outside of the laboratory). An extensive collection of naturally occurring populations of N. discreta in North
America would enable studies on population dynamics.
(^10) Batrachochytrium dendrobatitis. A representative of Chytridiomycota – the earliest fungal lineage – and of aquatic fungi that
degrade polymers. B. dendrobatidis is a recently described fungus thought to be the primary agent of the global amphibian
decline. It invades the top layers of amphibian skin cells, causing thickening of the keratinized tissues and thereby limiting
gas exchange.
(^11) Paxillus involutus. A common mycorrhizal fungus of trees. Mycorrhizal fungi of various types form intimate mutualistic rela-
tionships with about 90% of plants worldwide.