bg journal club 2010

Comparative Fungal Genomics Platform

Bongsoo ParkBioinformatics and Genomics

The Huck Institutes of the Life Sciences

Outline

• Introduction - Fungi • Fungal Genome Sequences• Construction of the CFGP Database• Examples of How to Use CFGP• Ongoing Work & Future Directions

Why fungi are important?

• Recyclers of organic matters• Production of foods (mushrooms, wine,

fermentation products)• Industrial enzymes, organic acids, and

pharmaceuticals • Major cause of plant diseases• Direct threat to human health

http://en.wikipedia.org/wiki/File:Fungi_collage.jpg

http://tolweb.org/fungi

http://tolweb.org/tree/

How many fungal species exist?Fungi Kingdom 100,000 described(1) 1,500,000 estimated(2)

Ascomycota 64163

Basidiomycota 31515

Blastocladiomycota 179

Chytridiomycota 706

Glomeromycota 169

Microsporidia 1300

Neocallimastigomycota 20

(1) Directory of the Fungi (Kirk et al. 2008, 10th Edition)(2) The fungal dimension of biodiversity: magnitude, significance, and conservation (Hawksworth DL. 2006, Mycological Research 95:641-55)

http://danny.oz.au/travel/iceland/p/3571-fungi.jpg

Fungal Genome Sequencing

• First fungal genome sequence (Yeast Saccharomyces cerevisiae; Ascomycota > Saccharomycotina)

http://www.wikipedia.org/Yeast

Strains Size (Mb) No. of ORFs

S. cerevisiae S288C 12.2 5898

S. cerevisiae RM11-1a 11.7 5383

S. cerevisiae YJM789 11.9 5471

Table 1. CFGP(Comparative Fungal Genomics Platform)

Fungi Kingdom CFGP (2008) CFGP(2010)

Ascomycota 52 89

Basidiomycota 8 15

Blastocladiomycota 0 1

Chytridiomycota 2 2

Glomeromycota 0 0

Microsporidia 0 3

Neocallimastigomycota 0 0

Zygomycota 1 3

63 113

Table 1. CFGP(Comparative Fungal Genomics Platform)

Progress in Fungal Genome Sequencing

Construction of the CFGP Database

CFGPNCBI

BroadInstitutes

TIGR

JGI WGSC

SangerInstitutes

Genoscope

Design of CFGP

J. Park, et al. Proceeding in Korean-Japan Joint Bioinformatics Conference in 2009

Construction of CFGP

PHP, Javascript, HTML, Ajax

Perl, C

MySQL, Linux OS system

Figure 1. CFGP(Comparative Fungal Genomics Platform)

Programs Description

BLAST Basic Local Alignment Sequence Tool

ClustalW Multiple Sequence Alignment

InterProScan Prediction of functional domain

SignalP 3.0 Prediction of signal peptide

PSORT II Prediction of subcellular localization

Middle Ware (C, Perl)

Blast.pl(Perl)

Blast(C)

User interface(PHP)

Middle Ware (C, Perl)

Blast.pl(Perl)

Blast(C)

User interface(PHP)

ClustalW(C)

Clustalw.pl(Perl)

Integration of new programs is easy.


BLAST Basic Local Alignment Sequence Tool

ClustalW Multiple Sequence Alignment

InterProScan Prediction of functional domain

SignalP 3.0 Prediction of signal peptide

PSORT II Prediction of subcellular localization

Integration of new programs is easy.

PHYLIP(DNAML, PROML, DNAPARS, PROTPARS)PHYML, MEME, tRNAScan-SE, mFOLD, SigCleave

SigPred, RPSP, ChloroP, TargetP, THHMM2, SecretomeP

User Interface

http://cfgp.snu.ac.kr/

Examples of How to Use CFGP



What is ‘Favorite’ function

• Virtual Cart for collecting sequences from the CFGP data warehouse

• Many analyses can be conducted in Favorite Workbench

• Make it easy to integrate additional bioinformatics tools into CFGP

Favorite Workbench

What is BLAST Matrix?

• BLAST Matrix allows simultaneous BLAST searches against genome sequences of multiple species.

• Provides a graphical overview of search results in the taxonomic framework of the searched species

Ongoing work & Future Directions

• Keep collecting published genome sequence data



• Link with phylogenetic and population genetic data from major plant pathogen groups (e.g., Phytophthora, Pythium, Fusarium)

Next Step of CFGP

• Keep collecting published sequence data• Comparative genomics tools for Fungal and

Oomycete community (Fusarium, Phytophthora, Pythium)

Cyberinfrastructure for Fusarium

• Fusarium Research Center at Penn State

Broad Institues of the Genome Sequencing



• Link with phylogenetic and population genetic data from major plant pathogen groups (e.g., Phytophthora, Pythium, Fusarium)

• Evolutionary studies of fungal gene families (e.g., cytochrome P450s, ABC transporters) and functional groups (e.g., transcription factors)

Thank you!

AcknowledgementsDr. Seogchan Kang, Penn State UniversityDr. Yong-Hwan Lee, Seoul National UniversityDr. David M. Geiser, Penn State UniversityJongsun Park, Seoul National University

Kang’s Lab membersDr. Hae-Seon KimVasileios BitasVenkatash Moktali

Supplementary

Fungal cell wall (Chitin)

(C8H13O5N)n

Plant cell wall (Cellulose)

(C6H10O5)n

http://en.wikipedia.org/

Supplementary

http://www.fungionline.org.uk/7sexual/5dikaryon.html

Saccharomyces cerevisiae

http://www.fusariumdb.org

CFGP Fungi sequences

Sequenced_Fungi.txt (113) CFGP 2.0


PHYLIP PHYLogeny Inference Package – Felsenstein

PHYML Fast, Accurate estimation of large PHYlogenies by Maximum Likelihood

MEME Discovering and analyzing DNA and protein sequence motifs

tRNAScan-SE A program for improved detection of transfer RNA genes in genomic sequence

mFOLD Prediction of nucleic acid folding and hybridization

SigCleave Reports on signal cleavage sites in a protein sequence

SigPred Signal Peptide Prediction

RPSP Prediction of signal peptides

ChloroP Prediction of chloroplast transit peptides and their cleavage sites

TargetP Prediction of potential subcellular location

THHMM2 Prediction of transmembrane helices in proteins

SecretomeP Prediction of Mammalian secretory proteins

Supplementary

Implementation of CFGP to different platforms

• 605 Users at Penn State Server• 408 Users at SNU Server

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