Download - BG Journal Club 2010
![Page 1: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/1.jpg)
Comparative Fungal Genomics Platform
Bongsoo ParkBioinformatics and Genomics
The Huck Institutes of the Life Sciences
![Page 2: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/2.jpg)
Outline
• Introduction - Fungi • Fungal Genome Sequences• Construction of the CFGP Database• Examples of How to Use CFGP• Ongoing Work & Future Directions
![Page 3: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/3.jpg)
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
![Page 5: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/5.jpg)
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
![Page 6: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/6.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)
![Page 7: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/7.jpg)
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
![Page 8: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/8.jpg)
Construction of the CFGP Database
CFGPNCBI
BroadInstitutes
TIGR
JGI WGSC
SangerInstitutes
Genoscope
![Page 9: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/9.jpg)
Design of CFGP
J. Park, et al. Proceeding in Korean-Japan Joint Bioinformatics Conference in 2009
![Page 10: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/10.jpg)
Construction of CFGP
PHP, Javascript, HTML, Ajax
Perl, C
MySQL, Linux OS system
Figure 1. CFGP(Comparative Fungal Genomics Platform)
![Page 11: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/11.jpg)
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
![Page 12: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/12.jpg)
Middle Ware (C, Perl)
Blast.pl(Perl)
Blast(C)
User interface(PHP)
![Page 13: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/13.jpg)
Middle Ware (C, Perl)
Blast.pl(Perl)
Blast(C)
User interface(PHP)
ClustalW(C)
Clustalw.pl(Perl)
Integration of new programs is easy.
![Page 14: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/14.jpg)
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
![Page 15: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/15.jpg)
User Interface
http://cfgp.snu.ac.kr/
![Page 17: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/17.jpg)
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
![Page 18: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/18.jpg)
Favorite Workbench
![Page 19: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/19.jpg)
Favorite Workbench
![Page 20: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/20.jpg)
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
![Page 21: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/21.jpg)
![Page 22: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/22.jpg)
![Page 23: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/23.jpg)
Ongoing work & Future Directions
• Keep collecting published genome sequence data
![Page 24: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/24.jpg)
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)
![Page 25: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/25.jpg)
Next Step of CFGP
• Keep collecting published sequence data• Comparative genomics tools for Fungal and
Oomycete community (Fusarium, Phytophthora, Pythium)
![Page 26: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/26.jpg)
![Page 27: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/27.jpg)
Cyberinfrastructure for Fusarium
• Fusarium Research Center at Penn State
Broad Institues of the Genome Sequencing
![Page 28: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/28.jpg)
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)
![Page 29: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/29.jpg)
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
![Page 30: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/30.jpg)
Supplementary
Fungal cell wall (Chitin)
(C8H13O5N)n
Plant cell wall (Cellulose)
(C6H10O5)n
http://en.wikipedia.org/
![Page 31: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/31.jpg)
Supplementary
http://www.fungionline.org.uk/7sexual/5dikaryon.html
![Page 32: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/32.jpg)
Saccharomyces cerevisiae
![Page 33: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/33.jpg)
![Page 34: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/34.jpg)
http://www.fusariumdb.org
![Page 35: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/35.jpg)
CFGP Fungi sequences
Sequenced_Fungi.txt (113) CFGP 2.0
![Page 36: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/36.jpg)
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
![Page 37: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/37.jpg)
![Page 38: BG Journal Club 2010](https://reader033.vdocuments.us/reader033/viewer/2022061206/5481e405b07959420c8b4646/html5/thumbnails/38.jpg)
Implementation of CFGP to different platforms
• 605 Users at Penn State Server• 408 Users at SNU Server