This document discusses the progress of fungal genomics. It notes that the sequencing of the yeast S. cerevisiae genome in 1996 revolutionized work in yeast genetics. The Fungal Genome Initiative was launched in 2000 to sequence genomes of fungi throughout the kingdom. To date, high quality draft genomes have been published for 10 fungi. Fungal genomes range in size from 12-40 Mb. Chromosomal genes make up the bulk of the genome. Mitochondrial, plasmid, and virus-like genes also contribute to the fungal phenotype. Transposons are rare in filamentous fungi. The S. cerevisiae genome was discussed as an example, noting its 16 chromosomes, 6183 genes, and circular 2 μm plasmid

1. by
Muhammad Getso
Department of Medical Mycology, TUMS-Iran

2. Background
• The over 1.5 million members of the Fungal Kingdom
are known to impact nearly all other forms of life either
directly or indirectly (Hawksworth 1991).
• The relationship can be beneficial (biotransformations,
fermentation and the production of antibiotics) or extremely
detrimental (devastating impacts of mycoses or
mycotoxins)[Moss 1987].
• Despite the importance and utility of fungi, little was known
about the genetics, until recently when there has been an
explosion in fungal genomics that has greatly expanded the
horizon of the genetic and physiological diversity of fungi.

3. • The era of fungal genomics was ushered in by the sequencing of
the complete genome of the yeast S. cereviseae, reported in 1996.
• This milestone revolutionized work in yeast and enabled the first
global studies of eukaryotic gene function and expression.
• However, the yeast genome sequence provided only a limited
glimpse of the biological diversity of the fungal kingdom.
• The progress in sequencing fungal genomes was initially slow.
• Accelerate by the luncheon of Fungal Genome Initiative (FGI) by a
consortium of mycologists in collaboration with MIT Center for
Genome, in 2000 (http://www.broad.mit.edu/annotation/fgi/)
Introduction

4. • The goal of the FGI was to sequence the genomes of
fungi from throughout the kingdom
• Currently the “high-quality draft“ genome
sequences of ten fungi have been published,
including Saccharomyces cerevisiae, Neurospora crassa,
Emericella nidulans, Schizosaccharomyces pombe,
Magnaporthe grisea (the rice blast pathogen), and
Phanerochaete chrysosporium (wood-rotting fungus).
• The first four of these are Ascomycota with well-
mapped chromosomes, providing a basis for
combining classical and molecular genetics.

5. Fungal genomics
• The genome of fungi includes all the genetic information
encoded by the chromosomal genes and extra
chromosomal components
• Each of these can contribute significantly to the phenotype
of fungi.
Fungal Genome
Extrachromosomal:
o Mitochondrial
o Plasmids
o Fungal virus gene
Chromosomal
genes

6. Fungal Chromosomes and
Chromosomal genes
• Fungal genomes are simple and compact.
• Sizes range from 12,068 kb (S. cerevisiae), 22,540 kb (T.
verrucosum), 28,467 kb (P. marneffei) and 32,228 kb (P.
chrysogenum).
• The small genome size of fungi is because they have little
multicopy (reiterated)DNA . The only reiterated DNA codes
mainly for rRNA, tRNA and chromosomal proteins.
• The haploid chromosome count of most fungi seems to lie
between 6 and 16, [3--40].

7. Approximate Genomic size of some fungi
Fungus Genome size (Mb)
Aspergillus fumigatus 30
A. niger 30
Candida albicans 16
Cryptococcus neoformans 21
Aspergillus nidulans 28
Neurospora crassa 40
Phanerochaete chrysosporium 40
Schizosaccharomyces pombe 1
Phytophthora sojae 62
Pneumocystis jiroveci 7.7
Saccharomyces cerevisiae 12

8. Fungal Chromosomes and Chromosomal genes
• Most fungi are haploid, but the Oomycota are
diploid.
• A few fungi can alternate between haploid and
diploid somatic phases, and
• Some yeasts (e.g. Candida albicans) are
permanently diploid.
• Some fungi and fungus-like organisms have
polyploid series

9. Yeast genome (S. cerevisiae)
• The 12 Mb genome of Saccharomyces cerevisiae is
clustered into 16 chromosomes (of 200–2200 kb in size).
• Has 6183 open-reading frames (ORFs), of which 5885 are
predicated to be protein-coding genes.
• The fungi transcribe a substantial (50–60%) amount of the
nuclear DNA into mRNA.
• The protein-encoding genes contain noncoding DNA
sequences termed introns; excised before the mRNA is
translated into proteins.
• S. cerevisiae is has very few introns(introns of fungi are very
short ).

10. Mitochondrial genome
• Mitochondria contain a small circular DNA of
varying sizes.
• Fungal mitochondrial genomes are often in the
range of 19–121 kb
• The mitochondrial DNA of fungi has relation to
aging; because in several filamentous fungi
(Podospora, Neurospora, Aspergillus) a single
mutation in a single mitochondrion can lead to
senescence of the whole colony.

11. Plasmids and transposable elements
• Plasmids usually are closed-circular DNA molecules, capable
of autonomous replication. Can also be linear if the ends are
“capped”.
• Plasmids or plasmid-like DNAs have been found in several
fungi.
• The most notable example is the “two-micron” plasmid of S.
cerevisiae, so-called because of its 2 μm length as seen in
electron micrographs.
• This plasmid is a closed circular molecule of 6.3 kb, and it is
unusual because it is found in the nucleus.
• It has no known function (used to construct “vectors” ).

12. • Most fungal plasmids are found in the mitochondria.
• They include the linear DNA plasmids of Neurospora
crassa and N. intermedia.
• They show a degree of sequence homology to the
mitochondrial genome (??defective, excised segments of the
mitochondrial genes).
• Some other mitochondrial plasmids of Neurospora are
closed circular molecules with little or no homology to
the mitochondrial genome.
• They do not code for antibiotic resistance or
pathogenicity

13. Transposons
• Transposons (transposable elements) are short regions of DNA that
remain in the chromosome but encode enzymes for their own
replication.
• They produce RNA copies of themselves, and they encode the enzyme,
reverse transcriptase, which synthesizes new copies of DNA from this RNA
template (similar to retroviruses).
• The new copies of DNA can then insert at various points in the same or
other chromosomes, leading to alterations in gene expression.
• Transposons seem to be rare in filamentous fungi, but there are several
types in S. cerevisiae.
• The best studied of these are the chromosomal Ty elements; have no
function, except for self-perpetuation

14. Virus-like genes
• Electron micrographs of both the hyphae and the
fruitbodies showed the presence of many isometric virus-
like particles (VLPs) in over 150 species of fungi (Buck
1986).
• With a few notable exceptions, the presence of VLPs is not
associated with any obvious disorder (symptomless).
• VLPs are resident genetic elements of fungi because they
have no natural mechanism for crossing species barriers
but have shown to be associated with several yeasts cells
that produce killer toxins.

15. VPLs
• Studies on a range of fungi have shown that fungal viruses
(or VLPs) have similar basic features:
They are isometric particles, 25–50 nm diameter, with a
genome of dsRNA, a capsid composed of one major
polypeptide
The genome size is variable; ranges from about 3.5 to 10 kb.
In most fungi the VLPs are as crystalline arrays in the cytoplasm
of older hyphal regions, closely associated with ER.
 The natural means of transmission of VLPs is via the cytoplasm
during hyphal anastomosis (hyphal fusions) or by passage into
the asexual spores.

16. Saccharomyces cerevisiae Killer system
• The first studies showed the involvement of
i. Cytoplasmic genetic determinants
ii. The occurrence of double-stranded RNA (dsRNA) and
iii. associated virus-like particles (VLPs)
• S. cerevisiae killer toxins (K1,K2 and K28) are encoded by
different satellite dsRNAs (M1, M2 and M28) that are
cytoplasmically inherited and encapsidated in VLPs.
• For their replication and encapsidation, another
group of helper yeast viruses (L-A) is needed.

18. Selected References
1. Deacon, J. W. (2013). Fungal biology. John Wiley & Sons. Pp 158-181
2. Galagan, J. E., Henn, M. R., Ma, L. J., Cuomo, C. A., & Birren, B. (2005).
Genomics of the fungal kingdom: insights into eukaryotic biology. Genome
research, 15(12), 1620-1631.
3. Hausner, G. (2003). Fungal Mitochondrial Genomes. Fungal Genomics, 3, 101.
4. Yoder, O. C., & Turgeon, B. G. (2001). Fungal genomics and
pathogenicity. Current opinion in plant biology, 4(4), 315-321.
5. Barry, E. G. (1996). Fungal chromosomes. Journal of Genetics, 75(3), 255-263.