Fungal genomicsbongsoo final

Bongsoo ParkOctober 6, 2010

Bioinformatics & Genomics

Fungal Genomics

Section 2

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Section 4

Section 1

Section 5

Contents

BackgroundsWhy fungi?

Section 1

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)



http://en.wikipedia.org/wiki/Prokaryotae



Fungi

Food , Fermentatione.g. Mushroom

Baker’s Yeast

AntibioticDiscovery

e.g. Pennicillin




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



Fungi

Ecological roleRecyling of dead

plants and animals

Scientific valueEukaryotic cell model Yeast (S. cerevisiae)


Baker’s Yeast

AntibioticDiscovery

e.g. Pennicillin


http://classes.dma.ucla.edu/Winter06/161B/projects/tonyau/ps2/1/index.html


http://www.csb.ethz.ch/research/dynamic

Easily culturedRapidly reproduced



Fungi

Ecological roleRecyling of dead

plants and animals

Scientific valueEukaryotic cell model Yeast (S. cerevisiae)

Plant Pathogense.g. Rice – M. oryzaePotato – P. infestansTomato – F. oxysporumCerials – F. graminearum

Pathogen and Toxins many harmful toxins


Beer, Wine, Baking

AntibioticDiscovery

e.g. Pennicillin


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


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


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 notatum1928, 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

Section 2

Section 3

Section 4

Section 1

Section 5

Contents

Section 2 Genome ResourcesAvailable databases

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cell&part=A1607

Genome Resources |available database?

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

228genomes

114fungal/oomycetespecies


Saccharomyces sp.

Agaricus sp.

Magnaporthe sp.Fusarium sp.Trichophyton sp.

Phytophthora sp.


http://fungalgenomes.org/wiki/Fungal_Genome_Links


http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html

Fungal Genomics Initiative at Broad Institutes

Funding :National Institutes of HealthNational Science FoundationUnited State Department of Agriculture


http://genome.jgi-psf.org/programs/fungi/index.jsf


http://fungi.ensembl.org/index.html

GENE CENTRIC SEARCH


http://genome.ucsc.edu/cgi-bin/hgGateway

CHROMOSOME CENTRIC VIEW

http://yeastmine.yeastgenome.org:8080/yeastmine/begin.do


Section 2

Section 3

Section 4

Section 1

Section 5

Contents

Fungal Biologye.g. Plant Pathogenic FungusSection 3

http://staff.vbi.vt.edu/brunolab/

Fungal Biology |Disease Triangle

Disease Triangle

http://apbiosemonefinalreview.pbworks.com/Fungi-%28Ch-31%29

Physical Weapone.g.) Appressorium formation

of Rice blast fungus

Chemical Weapone.g.) Cutinase EC(3.1.1.74)

Cell wall degradation

Fungal Biology |Physical and Chemical Weapon

http://140.254.84.203/wiki/index.php/Appressorium

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

Fungal Biology |Pathogen Diagnostics

1970-2010 40th Anniversary of Fusarium Rsearch Center

Fungal Biology |Pathogen Diagnostics

http://www.free-extras.com/images/tomato_plant-625.htm

http://science.howstuffworks.com/environmental/life/botany/wheat-info1.htmhttp://coo.fieldofscience.com/2007_12_01_archive.html

Fungal Biology |Formae speciales (Special forms)

F. oxy f. sp. lycopersici

F. oxy f. sp. cubense

F. oxysporum

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

Fungal Biology |Comparative Genomics

http://cfgp.riceblast.snu.ac.kr/main.php

Comparative Genomics Platform

Fungal Biology |Comparative Fungal Genomics Platform

http://cfgp.snu.ac.kr/�

http://cfgp.snu.ac.kr/�

Section 2

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Section 1

Section 5

Contents

Fusarium GenomicsPathogenicity Chromosomes?

Section 4

Interests of Fungal Biologists

Fusarium Genomics |Pathogenicity Chromosomes

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





a. Fusarium oxysporumb. Fusarium verticillioides syntenic alignmentc. Density of TEs



Segmental Duplications


Num

ber o

f TEs

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

OthersSINELINELTRsMITEHelitronMutatorhATimpalaPogo

Chromosomes


Chr 3,5,14,15 : Lineage-Specific Chromosomes

Section 2

Section 3

Section 4

Section 1

Section 5

Contents

Section 5

Challenging questionsOrigin of Lineage-Specific regions?

Challenging Questions |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



F. oxy ancestor

LS Chromosomes

F. oxy #1

F. oxy#2

F. oxy#3

F. oxy#4

Logical explanation 2.Duplication and Divergence #2



Logical explanation 3.Horizontal Gene Transfer #1

F. ancestor

LS Chromosomes

F. ver F. oxy F. gra F. sol?



F. oxy ancestor

LS Chromosomes

F. oxy #1

F. oxy#2

F. oxy#3

F. oxy#4

Logical explanation 3.Horizontal Gene Transfer #2


Challenging Questions |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.


Challenging Questions |Transfer of Chromosome 14

They proposed the HGT between F. oxysporum species. This huge

chromosomal HGT is the first discovery in Nature.


F. oxy f. sp. lycopersici F. oxy f. sp. cubense

Challenging Questions |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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Fungal genomicsbongsoo final