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Bongsoo Park
October 6, 2010
Bioinformatics & Genomics
Fungal Genomics
Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Backgrounds
Whyfungi?
Section 1
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
http://www.tutorvist...
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
http://en.wikipedia....
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
Fungi
Food , Ferment...
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
http://www.sheknows....
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
Fungi
Ecological rol...
Background |Why fungi?
http://classes.dma.ucla.edu/Winter06/161B/projects/tonyau/ps2/1/index.html
Background |Why fungi?
http://www.csb.ethz.ch/research/dynamic
Easily cultured
Rapidly reproduced
http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes
Background |Why fungi?
Fungi
Ecological rol...
Background |Why fungi?
 Characteristic symptoms of the rice blast
disease caused by Magnaporthe oryzae
 Annual loss of r...
Background |Why fungi?
http://letmeget.com/blog/different-types-skin-diseases
Fungi > Ascomytoca - Trichophyton
http://www...
Background |Why fungi?
1855
2010
1996, First eukaryotic genome sequencing, Saccharomyces cerevisiae
2010, Fusarium genome ...
Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Section 2
GenomeResources
Availabledatabases
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cell&part=A1607
GenomeResources |available database?
Park et al., (2008) CFGP: Comparative Fungal Genomics Platform. Nucleic Acid Research, 36, D562-D571.
Jung and Park et al....
GenomeResources |available database?
http://fungalgenomes.org/wiki/Fungal_Genome_Links
GenomeResources |available database?
http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html
Fungal ...
GenomeResources |available database?
http://genome.jgi-psf.org/programs/fungi/index.jsf
GenomeResources |available database?
http://fungi.ensembl.org/index.html
GENE CENTRIC SEARCH
GenomeResources |available database?
http://genome.ucsc.edu/cgi-bin/hgGateway
CHROMOSOME CENTRIC VIEW
http://yeastmine.yeastgenome.org:8080/yeastmine/begin.do
GenomeResources |available database?
Section 2
Section 3
Section 4
Section 1
Section 5
Contents
FungalBiology
e.g.PlantPathogenicFungusSection 3
http://staff.vbi.vt.edu/brunolab/
FungalBiology |Disease Triangle
Disease
Triangle
http://apbiosemonefinalreview.pbworks.com/Fungi-%28Ch-31%29
Physical Weapon
e.g.) Appressorium formation
of Rice blast fun...
http://www.plant-care.com/fungicides-a-part-of-a-disease-control-program.html http://apbiosemonefinalreview.pbworks.com/Fu...
1970-2010 40th Anniversary of Fusarium Rsearch Center
FungalBiology |Pathogen Diagnostics
http://www.free-extras.com/images/tomato_plant-625.htm
http://science.howstuffworks.com/environmental/life/botany/wheat-in...
FIGURE 1. Phylogenetic relationship of four Fusarium species in relation to other
ascomycete fungi and phenotypic variatio...
http://cfgp.riceblast.snu.ac.kr/main.php
Comparative Genomics Platform
FungalBiology |Comparative Fungal Genomics Platform
Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Fusarium Genomics
PathogenicityChromosomes?
Section 4
InterestsofFungalBiologists
FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
a. Fusarium o...
FusariumGenomics |Pathogenicity Chromosomes
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
Segmental Dup...
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 1...
Section 2
Section 3
Section 4
Section 1
Section 5
Contents
Section 5
Challengingquestions
OriginofLineage-Specificregions?
ChallengingQuestions |Logical explanation 2.1
F. oxy ancestor
LS Chromosomes
F. oxy
#1
F. oxy
#2
F. oxy
#3
F. oxy
#4
Logic...
ChallengingQuestions |Logical explanation 2.2
F. oxy ancestor
LS Chromosomes
F. oxy
#1
F. oxy
#2
F. oxy
#3
F. oxy
#4
Logic...
ChallengingQuestions |Logical explanation 3.1
Logical explanation 3.
Horizontal Gene Transfer #1
F. ancestor
LS Chromosome...
ChallengingQuestions |Logical explanation 3.2
F. oxy ancestor
LS Chromosomes
F. oxy
#1
F. oxy
#2
F. oxy
#3
F. oxy
#4
Logic...
ChallengingQuestions |Transfer of Chromosome 14
Chromosome 14
SIX1, SIX2
SIX5, SIX6, SIX7
They are the plant-secreted prot...
ChallengingQuestions |Transfer of Chromosome 14
They proposed the HGT between
F. oxysporum species. This huge
chromosomal ...
ChallengingQuestions |Future Direction
Fungi, Friend or Enemy?
L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature...
Fungal genomicsbongsoo final
Fungal genomicsbongsoo final
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Transcript of "Fungal genomicsbongsoo final"

  1. 1. Bongsoo Park October 6, 2010 Bioinformatics & Genomics Fungal Genomics
  2. 2. Section 2 Section 3 Section 4 Section 1 Section 5 Contents Backgrounds Whyfungi? Section 1
  3. 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. 4. http://www.sheknows.com/food-and-recipes/articles/805470/wild-mushroom-recipes Background |Why fungi? http://en.wikipedia.org/wiki/Prokaryotae
  5. 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. 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. 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. 8. Background |Why fungi? http://classes.dma.ucla.edu/Winter06/161B/projects/tonyau/ps2/1/index.html
  9. 9. Background |Why fungi? http://www.csb.ethz.ch/research/dynamic Easily cultured Rapidly reproduced
  10. 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. 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. 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. 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. 14. Section 2 Section 3 Section 4 Section 1 Section 5 Contents Section 2 GenomeResources Availabledatabases
  15. 15. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cell&part=A1607 GenomeResources |available database?
  16. 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. 17. GenomeResources |available database? http://fungalgenomes.org/wiki/Fungal_Genome_Links
  18. 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. 19. GenomeResources |available database? http://genome.jgi-psf.org/programs/fungi/index.jsf
  20. 20. GenomeResources |available database? http://fungi.ensembl.org/index.html GENE CENTRIC SEARCH
  21. 21. GenomeResources |available database? http://genome.ucsc.edu/cgi-bin/hgGateway CHROMOSOME CENTRIC VIEW
  22. 22. http://yeastmine.yeastgenome.org:8080/yeastmine/begin.do GenomeResources |available database?
  23. 23. Section 2 Section 3 Section 4 Section 1 Section 5 Contents FungalBiology e.g.PlantPathogenicFungusSection 3
  24. 24. http://staff.vbi.vt.edu/brunolab/ FungalBiology |Disease Triangle Disease Triangle
  25. 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. 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. 27. 1970-2010 40th Anniversary of Fusarium Rsearch Center FungalBiology |Pathogen Diagnostics
  28. 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. 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. 30. http://cfgp.riceblast.snu.ac.kr/main.php Comparative Genomics Platform FungalBiology |Comparative Fungal Genomics Platform
  31. 31. Section 2 Section 3 Section 4 Section 1 Section 5 Contents Fusarium Genomics PathogenicityChromosomes? Section 4
  32. 32. InterestsofFungalBiologists
  33. 33. FusariumGenomics |Pathogenicity Chromosomes L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
  34. 34. FusariumGenomics |Pathogenicity Chromosomes L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850
  35. 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. 36. FusariumGenomics |Pathogenicity Chromosomes L-J Ma et al. Nature 464, 367-373 (2010) doi:10.1038/nature08850 Segmental Duplications
  37. 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. 38. Section 2 Section 3 Section 4 Section 1 Section 5 Contents Section 5 Challengingquestions OriginofLineage-Specificregions?
  39. 39. 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
  40. 40. 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
  41. 41. 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
  42. 42. 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
  43. 43. 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
  44. 44. 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
  45. 45. 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
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