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Fungal genomicsbongsoo final

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  • 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?
  • 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. 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. 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. 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. 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. 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. 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