1. Bongsoo Park
October 6, 2010
Bioinformatics & Genomics
Fungal Genomics

2. Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Backgrounds
Whyfungi?
Section 1

3. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
http://www.tutorvista.com/biology/r-h-whittaker-5-kingdom-classification
 1758 Linnaeus
Two Kingdom Classfication
(Plantae and Animalia)
 1866 Haeckel
Three Kingdom Classification
(Plantae, Animalia, and Protista)
 1969 Whittaker
New Kingdom - Fungi
 1938 Copeland
New Kingdom – Monera
(Prokaryotae)

4. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
http://en.wikipedia.org/wiki/Prokaryotae

5. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
Fungi
Food , Fermentation
e.g. Mushroom
Baker’s Yeast
Antibiotic
Discovery
e.g. Pennicillin

6. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
 Fungi > Basidiomycota
 Mushroom
http://en.wikipedia.org/wiki/File:ChampignonMushroom.jpg
Agaricus bisporus
 Fungi > Ascomycota
 Baker’s yeast (Saccharomyces cerevisiae)
 Fungi > Ascomycota
 Penniicillum notatum produces penicillin
http://en.wikipedia.org/wiki/Yeast http://www.waterscan.rs/images/virusi-bakterije//bacterie-penicillium.jpg

7. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
Fungi
Ecological role
Recyling of dead
plants and animals
Scientific value
Eukaryotic cell model
Yeast (S. cerevisiae)
Food , Fermentation
e.g. Mushroom
Baker’s Yeast
Antibiotic
Discovery
e.g. Pennicillin

8. Background |Why fungi?
http://classes.dma.ucla.edu/Winter06/161B/projects/tonyau/ps2/1/index.html

9. Background |Why fungi?
http://www.csb.ethz.ch/research/dynamic
Easily cultured
Rapidly reproduced

10. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
Fungi
Ecological role
Recyling of dead
plants and animals
Scientific value
Eukaryotic cell model
Yeast (S. cerevisiae)
Plant Pathogens
e.g. Rice – M. oryzae
Potato – P. infestans
Tomato – F. oxysporum
Cerials – F. graminearum
Pathogen and Toxins
many harmful toxins
Food , Fermentation
e.g. Mushroom
Beer, Wine, Baking
Antibiotic
Discovery
e.g. Pennicillin

11. Background |Why fungi?
 Characteristic symptoms of the rice blast
disease caused by Magnaporthe oryzae
 Annual loss of rice by the blast fungus is
billon dollars all over the world
 Fungi is major plant pathogen
Images : Fungal Plant Pathogen Lab at Seoul National University
 Oomycete (Fungal-like) Pathogen
 Phytophthora infestans
 Irish Potato Famine (1845-1852)
http://vegetablemdonline.ppath.cornell.edu/factsheets/Potato_Detection.htm

12. Background |Why fungi?
http://letmeget.com/blog/different-types-skin-diseases
Fungi > Ascomytoca - Trichophyton
http://www.schmidtandclark.com/renu-moistureloc
Fungi > Ascomytoca - Fusarium
 Fumonisin is a mycotoxin from
fusarium infected kernels - neural
disorder of mice
http://agronomyday.cropsci.illinois.edu/2002/fumonisin/index.html

13. Background |Why fungi?
1855
2010
1996, First eukaryotic genome sequencing, Saccharomyces cerevisiae
2010, Fusarium genome sequenced at MIT Broad Institutes
2009, 70 different strains of Saccharomyces cerevisiae sequenced
1928, Alexander Fleming, Penicillium notatum
1928, Mushroom cultivation in Pennsynvania,
1928, Mushroom Science in Buckhout at Penn State University
1969, Whittaker, Fungal Kingdom Defined
1845-1852, Irish Potato Famine, Phytophthora infestans
1915-1927, Pennicillin reported

14. Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Section 2
GenomeResources
Availabledatabases

15. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cell&part=A1607
GenomeResources |available database?

16. Park et al., (2008) CFGP: Comparative Fungal Genomics Platform. Nucleic Acid Research, 36, D562-D571.
Jung and Park et al., SNUGB: a versatile genome browser supporting comparative and functional fungal genomics, BMC Genomics, 9, 586
228
genomes
114
fungal/oomycete
species
GenomeResources |available database?
Saccharomyces sp.
Agaricus sp.
Magnaporthe sp.
Fusarium sp.
Trichophyton sp.
Phytophthora sp.

17. GenomeResources |available database?
http://fungalgenomes.org/wiki/Fungal_Genome_Links

18. GenomeResources |available database?
http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html
Fungal Genomics Initiative at Broad Institutes
Funding :
National Institutes of Health
National Science Foundation
United State Department of Agriculture

19. GenomeResources |available database?
http://genome.jgi-psf.org/programs/fungi/index.jsf

20. GenomeResources |available database?
http://fungi.ensembl.org/index.html
GENE CENTRIC SEARCH

21. GenomeResources |available database?
http://genome.ucsc.edu/cgi-bin/hgGateway
CHROMOSOME CENTRIC VIEW

22. http://yeastmine.yeastgenome.org:8080/yeastmine/begin.do
GenomeResources |available database?

23. Section 2
Section 3
Section 4
Section 1
Section 5
Contents
FungalBiology
e.g.PlantPathogenicFungusSection 3

24. http://staff.vbi.vt.edu/brunolab/
FungalBiology |Disease Triangle
Disease
Triangle

25. http://apbiosemonefinalreview.pbworks.com/Fungi-%28Ch-31%29
Physical Weapon
e.g.) Appressorium formation
of Rice blast fungus
Chemical Weapon
e.g.) Cutinase EC(3.1.1.74)
Cell wall degradation
FungalBiology |Physical and Chemical Weapon
http://140.254.84.203/wiki/index.php/Appressorium

26. http://www.plant-care.com/fungicides-a-part-of-a-disease-control-program.html http://apbiosemonefinalreview.pbworks.com/Fungi-%28Ch-31%29
Accurate Diagnostics is essential !!!
1) Morphology
2) DNA Markers
FungalBiology |Pathogen Diagnostics

27. 1970-2010 40th Anniversary of Fusarium Rsearch Center
FungalBiology |Pathogen Diagnostics

28. http://www.free-extras.com/images/tomato_plant-625.htm
http://science.howstuffworks.com/environmental/life/botany/wheat-info1.htm
http://coo.fieldofscience.com/2007_12_01_archive.html
FungalBiology |Formae speciales (Special forms)
F. oxy f. sp. lycopersici
F. oxy f. sp. cubense
F. oxysporum

29. FIGURE 1. Phylogenetic relationship of four Fusarium species in relation to other
ascomycete fungi and phenotypic variation among the four Fusarium species.
http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html
FungalBiology |Comparative Genomics

30. http://cfgp.riceblast.snu.ac.kr/main.php
Comparative Genomics Platform
FungalBiology |Comparative Fungal Genomics Platform

31. Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Fusarium Genomics
PathogenicityChromosomes?
Section 4

32. InterestsofFungalBiologists

33. FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

34. FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

35. FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
a. Fusarium oxysporum
b. Fusarium verticillioides syntenic alignment
c. Density of TEs

36. FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
Segmental Duplications

37. FusariumGenomics |Pathogenicity Chromosomes
NumberofTEs
0
50
100
150
200
250
300
350
400
450
500
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Others
SINE
LINE
LTRs
MITE
Helitron
Mutator
hAT
impala
Pogo
Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
Chr 3,5,14,15 : Lineage-Specific Chromosomes

38. Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Section 5
Challengingquestions
OriginofLineage-Specificregions?

40. ChallengingQuestions |Logical explanation 2.1
F. oxy ancestor
LS Chromosomes
F. oxy
#1
F. oxy
#2
F. oxy
#3
F. oxy
#4
Logical explanation 2.
Duplication and Divergence #1
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

41. ChallengingQuestions |Logical explanation 2.2
F. oxy ancestor
LS Chromosomes
F. oxy
#1
F. oxy
#2
F. oxy
#3
F. oxy
#4
Logical explanation 2.
Duplication and Divergence #2
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

42. ChallengingQuestions |Logical explanation 3.1
Logical explanation 3.
Horizontal Gene Transfer #1
F. ancestor
LS Chromosomes
F. ver F. oxy F. gra F. sol?
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

43. ChallengingQuestions |Logical explanation 3.2
F. oxy ancestor
LS Chromosomes
F. oxy
#1
F. oxy
#2
F. oxy
#3
F. oxy
#4
Logical explanation 3.
Horizontal Gene Transfer #2
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

44. ChallengingQuestions |Transfer of Chromosome 14
Chromosome 14
SIX1, SIX2
SIX5, SIX6, SIX7
They are the plant-secreted proteins.
Chromosome 14 could be responsible for
pathogenicity of Fusarium oxysporum in
tomato wilt.
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850

45. ChallengingQuestions |Transfer of Chromosome 14
They proposed the HGT between
F. oxysporum species. This huge
chromosomal HGT is the first discovery
in Nature.
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
F. oxy f. sp. lycopersici F. oxy f. sp. cubense

46. ChallengingQuestions |Future Direction
Fungi, Friend or Enemy?
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850http://evolution.berkeley.edu/evosite/misconceps/IIBcrisis.shtml