BG Journal Club 2010
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Transcript of 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
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.
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
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/
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
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
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
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)
• 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
Programs Description
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