Phytophthora DatabasePhytophthora Databasehttp://www.phytophthoradb.orghttp://www.phytophthoradb.org

cyber-infrastructure for plant pathogens

13th August 2008Bongsoo ParkDepartment of Plant PathologyPennsylvania State University

Plant Pathology in GeneralPlant Pathology in General

“The scientific study of plant diseases caused by pathogens (infectious diseases) and environmental conditions (physiological factors)”

Host

Disease Environmental Factors

Strengths in Plant Pathology at Penn Strengths in Plant Pathology at Penn StateState

Mushroom Science / MycologyCulture Collection CentersMolecular Host-Plant Interaction Internet Database

The above result comes from Discussion on strategic meeting 15th July in Buckhout Laboratory

Why ‘Phytophthora’ genus is Why ‘Phytophthora’ genus is important?important?

High virulenceAbility to spread rapidlyDestructive potential of Phytophthora

diseaseNickname? ‘Plant Destroyer’

Ex) Irish potato famine (P. infestans)Sudden oak death in U.S (P. ramonum)Diseases on ornamental plants in Europe

Sudden oak death in Sudden oak death in CaliforniaCalifornia

Phytophthora infestansPhytophthora infestans

MorphologyHas been important.

Global importance and Global importance and collaborationscollaborations

Major crop loss caused by introduced pathogens (Agrious, 2005)Fund by USDA

What I have done so far?What I have done so far? Digital Library on Phytophthora species Construction for isolate database Construction for sequence database using data

from many collaborators in United States (USDA, PDA, Universities)

Integration molecular systematic &bioinformatic tools

(BLAST, ClustalW, and Phylogenetic programs)

Web site constructionWeb site construction

Phylogenetic Analysis on Phylogenetic Analysis on PhytophthoraPhytophthora

A multi-locus phylogeny for Phytophthora utilizing markersderived from complete genome sequences. Jaime E. Blair et al

What I’m doing right now?What I’m doing right now?D.B. QUALITY - Curation works on ITS marker sequences

D.B. EXPANSION - DB architecture in PD can be easily implemented to

other plant pathogen groups (e.g. Pythium, Fusarium)D.B. ANALYSIS – DNA BARCODE? - Phytophthora species specific oligos generation

D.B. FUTURE? - Wikipedia for Plant Pathology; Participation

members in community

Database curationDatabase curation

Phytophthora researchers begun to access the database at the same time with GenBank.

The sub-party databases having many professionals must be important to maintain the database.

GenBank PD

1837(More & Accurate)

1517(Accessibility)

?

Database expansionDatabase expansion

DNA BARCODE; Why ITS has DNA BARCODE; Why ITS has been utilized in systematics?been utilized in systematics?The internal transcribed spacer(ITS) regions

of ribosomal genes are especially useful targets for species-specific primers

1)High copy number increases detection sensitivity

2)Sequence variability among pathogen species

3)Universal primers at conserved portions of ribosomal DNA

ITS Figure on PDITS Figure on PD

ITS Sequence in GeneralITS Sequence in General

ITS1 ITS2

Design for Species specific Design for Species specific Nucleotide oligosNucleotide oligos

15nt

Region 4

Region 1

Specific region 3Specific region 2

Region 1

Specific region 2

Specific region 3

Region 4

Cyber-infrastructure for Plant Cyber-infrastructure for Plant PathologyPathologyMolecular Data ResourceDigital LibraryReference ResourcePlant Disease Image BankSocial Network PlatformWikipedia for Plant Pathology

- It needs many collaborations in community

AcknowledgementsAcknowledgements

Seogchan Kang, Penn State UniversityYong-Hwan Lee, Seoul National University Jongsun Park, Seoul National University Jamie E. Blair, Franklin & Marshall CollegeMichele A. Mansfield, Penn State University

USDA-NRI Plant Biosecurity program (2005-35605-15393 and 2008-55605-18773)

Thank you~!