Phytophthora Database http://www.phytophthoradb.org cyber-infrastructure for plant pathogens 13 th  August 2008 Bongsoo Pa...
Plant Pathology in General <ul><li>“ The scientific study of plant diseases caused by pathogens (infectious diseases) and ...
Strengths in Plant Pathology at Penn State <ul><li>Mushroom Science / Mycology </li></ul><ul><li>Culture Collection Center...
Why ‘Phytophthora’ genus is important? <ul><li>High virulence </li></ul><ul><li>Ability to spread rapidly </li></ul><ul><l...
Sudden oak death in California
Phytophthora infestans Morphology Has been important.
Global importance and collaborations Major crop loss caused by introduced pathogens (Agrious, 2005) Fund by USDA
What I have done so far? <ul><li>Digital Library on  Phytophthora  species </li></ul><ul><li>Construction for isolate data...
Web site construction
Phylogenetic Analysis on  Phytophthora   A multi-locus phylogeny for  Phytophthora  utilizing markers derived from complet...
What I’m doing right now? <ul><li>D.B. QUALITY  </li></ul><ul><li>- Curation works on ITS marker sequences </li></ul><ul><...
Database curation <ul><li>Phytophthora  researchers begun to access the database at the same time with GenBank. </li></ul>...
Database expansion
DNA BARCODE; Why ITS has been utilized in systematics? <ul><li>The internal transcribed spacer(ITS) regions of ribosomal g...
ITS Figure on PD
ITS Sequence in General ITS1 ITS2
Design for Species specific Nucleotide oligos 15nt Region 4 Region 1 Specific region 3 Specific region 2 Region 1 Specific...
Cyber-infrastructure for Plant Pathology <ul><li>Molecular Data Resource </li></ul><ul><li>Digital Library </li></ul><ul><...
Acknowledgements <ul><li>Seogchan Kang, Penn State University </li></ul><ul><li>Yong-Hwan Lee, Seoul National University <...
<ul><li>Thank you~! </li></ul>
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Bg Seminar(Phytophthora Db)

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Bg Seminar(Phytophthora Db)

  1. 1. Phytophthora Database http://www.phytophthoradb.org cyber-infrastructure for plant pathogens 13 th August 2008 Bongsoo Park Department of Plant Pathology Pennsylvania State University
  2. 2. Plant Pathology in General <ul><li>“ The scientific study of plant diseases caused by pathogens (infectious diseases) and environmental conditions (physiological factors)” </li></ul>Host Disease Environmental Factors
  3. 3. Strengths in Plant Pathology at Penn State <ul><li>Mushroom Science / Mycology </li></ul><ul><li>Culture Collection Centers </li></ul><ul><li>Molecular Host-Plant Interaction </li></ul><ul><li>Internet Database </li></ul><ul><li>The above result comes from Discussion on strategic meeting 15 th July in Buckhout Laboratory </li></ul>
  4. 4. Why ‘Phytophthora’ genus is important? <ul><li>High virulence </li></ul><ul><li>Ability to spread rapidly </li></ul><ul><li>Destructive potential of Phytophthora disease </li></ul><ul><li>Nickname? ‘Plant Destroyer’ </li></ul><ul><li>Ex) Irish potato famine ( P. infestans ) </li></ul><ul><li>Sudden oak death in U.S ( P. ramonum ) </li></ul><ul><li>Diseases on ornamental plants in Europe </li></ul>
  5. 5. Sudden oak death in California
  6. 6. Phytophthora infestans Morphology Has been important.
  7. 7. Global importance and collaborations Major crop loss caused by introduced pathogens (Agrious, 2005) Fund by USDA
  8. 8. What I have done so far? <ul><li>Digital Library on Phytophthora species </li></ul><ul><li>Construction for isolate database </li></ul><ul><li>Construction for sequence database using data from many collaborators in United States (USDA, PDA, Universities) </li></ul><ul><li>Integration molecular systematic &bioinformatic tools </li></ul><ul><li>(BLAST, ClustalW, and Phylogenetic programs) </li></ul>
  9. 9. Web site construction
  10. 10. Phylogenetic Analysis on Phytophthora A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Jaime E. Blair et al
  11. 11. What I’m doing right now? <ul><li>D.B. QUALITY </li></ul><ul><li>- Curation works on ITS marker sequences </li></ul><ul><li>D.B. EXPANSION </li></ul><ul><li>- DB architecture in PD can be easily implemented to other plant pathogen groups (e.g. Pythium, Fusarium ) </li></ul><ul><li>D.B. ANALYSIS – DNA BARCODE? </li></ul><ul><li>- Phytophthora species specific oligos generation </li></ul><ul><li>D.B. FUTURE? </li></ul><ul><li>- Wikipedia for Plant Pathology; Participation members in community </li></ul>
  12. 12. Database curation <ul><li>Phytophthora researchers begun to access the database at the same time with GenBank. </li></ul><ul><li>The sub-party databases having many professionals must be important to maintain the database. </li></ul>GenBank PD 1837 (More & Accurate) 1517 (Accessibility) ?
  13. 13. Database expansion
  14. 14. DNA BARCODE; Why ITS has been utilized in systematics? <ul><li>The internal transcribed spacer(ITS) regions of ribosomal genes are especially useful targets for species-specific primers </li></ul><ul><li>High copy number increases detection sensitivity </li></ul><ul><li>Sequence variability among pathogen species </li></ul><ul><li>Universal primers at conserved portions of ribosomal DNA </li></ul>
  15. 15. ITS Figure on PD
  16. 16. ITS Sequence in General ITS1 ITS2
  17. 17. Design for Species specific Nucleotide oligos 15nt Region 4 Region 1 Specific region 3 Specific region 2 Region 1 Specific region 2 Specific region 3 Region 4
  18. 18. Cyber-infrastructure for Plant Pathology <ul><li>Molecular Data Resource </li></ul><ul><li>Digital Library </li></ul><ul><li>Reference Resource </li></ul><ul><li>Plant Disease Image Bank </li></ul><ul><li>Social Network Platform </li></ul><ul><li>Wikipedia for Plant Pathology </li></ul><ul><li>- It needs many collaborations in community </li></ul>
  19. 19. Acknowledgements <ul><li>Seogchan Kang, Penn State University </li></ul><ul><li>Yong-Hwan Lee, Seoul National University </li></ul><ul><li>Jongsun Park, Seoul National University </li></ul><ul><li>Jamie E. Blair, Franklin & Marshall College </li></ul><ul><li>Michele A. Mansfield, Penn State University </li></ul><ul><li>USDA-NRI Plant Biosecurity program </li></ul><ul><li>(2005-35605-15393 and 2008-55605-18773) </li></ul>
  20. 20. <ul><li>Thank you~! </li></ul>

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