The rapid expansion of global trade and human
travel has greatly accelerated the introduction of
non-endogenous pathogens ...
Sudden Oak Death
A good example illustrating the challenges we are
facing
?
2003
Disclaimers The content of this presentation
does not reflect a position or
policy of the Penn State
University or its aff...
Difficulties in accurately determining species/population
identity ->
Accurate determination of species/population identit...
Issues in Molecular Identification
Molecular identification is not a panacea.
• Your results may be as good as what you co...
“There are known knowns. These are
things we know that we know. There are
known unknowns. That is to
say, there are things...
Limited efforts and mechanisms to support global
cooperation and knowledge integration->
Mapping and documenting the diver...
Issues in Molecular Identification
Molecular identification is not a panacea.
• Your results may be as good as what you co...
Phytophthora Database
Cyberinfrastructure supporting identification and
monitoring of Phytophthora species
PCR amplificati...
•Penn State: J. Blair, S. Park, N. Veeraraghavan, M. Mansfield
& B. Park
•UC-Riverside: M. Peiman
•NC State: M. Green
•Wes...
Specific Objectives of the PD Project
To establish a comprehensive phylogenetic
framework for the genus Phytophthora.
To b...
Progress
Development of new phylogenetic markers
based on the genome sequences of P. ramorum,
P. capsici, P. sojae and P. ...
Organization of the Pytophthora Database
Park et al. Plant Disease 2008
C
Species Information Page
Functionality of the Pytophthora Database
Data Submission
BLAST Search
Virtual Gel
Sequence Alignment Phylogenetic Tree
Da...
Functionality of the Pytophthora Database
On-going Work
Linking isolate data from genome to ecosystem
Global Virtual Network of Plant Pathologists
North
America
South
America
Africa
Europe
Asia
GPN
(V) GIS
(III)Diagnostic To...
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Kang Fighting Phytophthora 08

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2008 APS Meeting

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Kang Fighting Phytophthora 08

  1. 1. The rapid expansion of global trade and human travel has greatly accelerated the introduction of non-endogenous pathogens and pests. The global climate change influences pathogen communities both directly and indirectly
  2. 2. Sudden Oak Death A good example illustrating the challenges we are facing ? 2003
  3. 3. Disclaimers The content of this presentation does not reflect a position or policy of the Penn State University or its affiliates. I do not endorse any wrong perception you might get from my presentation. These messages were paid for by the Swift Fungi For Truth.
  4. 4. Difficulties in accurately determining species/population identity -> Accurate determination of species/population identity is critical for risk assessment and the implementation of regulatory measures and appropriate disease control strategies. Challenge 1 QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture.
  5. 5. Issues in Molecular Identification Molecular identification is not a panacea. • Your results may be as good as what you compared with (legacy errors and problems). • Different genes may tell different stories. What is species? • Biological, morphological, and phylogenetic species concepts. • They overlap but not perfectly. Biological/geospatial contexts are critical. • Host and geographic origins of new isolates. • Pathological and morphological phenotypes.
  6. 6. “There are known knowns. These are things we know that we know. There are known unknowns. That is to say, there are things that we know we don't know. But there are also unknown unknowns. There are things we don't know we don't know.” - Donald Rumsfeld - Challenge 2 Limited understanding of pathogen diversity in nature -> There exist many “known knowns, known unknowns & unknown unknowns” threatening agricultural and ecological systems.
  7. 7. Limited efforts and mechanisms to support global cooperation and knowledge integration-> Mapping and documenting the diversity, distribution, and biology of major pathogens worldwide and sharing this information are essential to improve our ability to track and manage pathogens. Challenge 3
  8. 8. Issues in Molecular Identification Molecular identification is not a panacea. • Your results may be as good as what you compared with (legacy errors and problems). • Different genes may tell different stories. What is species? • Biological, morphological, and phylogenetic species concepts. • They overlap but not perfectly. Biological/geospatial contexts are critical. • Host and geographic origins of new isolates. • Pathological and morphological phenotypes.
  9. 9. Phytophthora Database Cyberinfrastructure supporting identification and monitoring of Phytophthora species PCR amplification of multiple marker genes DNA from known pathogen isolates DNA sequencing Genetic fingerprints for individual isolates Phenotypes (such as morphology, geographic & host of origin, host range, virulence, drug resistance, toxin profile) of known isolates 8470 NI909 QUERY 1152 ML-91 A119 91T16 JP34 Py-D P.P. infestansinfestans Principal Investigators Penn State: Seogchan Kang, David Geiser & Izabela Makalowska UC-Riverside: Mike Coffey North Carolina State University: Kelly Ivors USDA-ARS: Frank Martin & Kerry O’Donnell USDA-NRI Plant Biosecurity www.phytophthoradb.org
  10. 10. •Penn State: J. Blair, S. Park, N. Veeraraghavan, M. Mansfield & B. Park •UC-Riverside: M. Peiman •NC State: M. Green •West Virginia: Y. Balci •PA Dept of Ag: S. H. Kim & E. Nikolaeva •Seoul National University: Y. Lee, K. Jung & J. Park •USDA-ARS SBML: A. Rossman, D. Farr & E. Cline •APS Press: D. Erwin & O. Ribeiro
  11. 11. Specific Objectives of the PD Project To establish a comprehensive phylogenetic framework for the genus Phytophthora. To build a cyberinfrastructure that archives the genotypes, phenotypes, and distribution of individual Phytophthora species/isolates and provides data analysis and visualization tools. To develop and optimize molecular diagnostic tools for detecting and identifying Phytophthora species.
  12. 12. Progress Development of new phylogenetic markers based on the genome sequences of P. ramorum, P. capsici, P. sojae and P. infestans. Conducted a genus-wide phylogenetic analysis using representative species/isolates. Genotypic characterization of ~3,000 isolates (>90 species) within the genus. Establishment of the Phytophthora Database.
  13. 13. Organization of the Pytophthora Database Park et al. Plant Disease 2008
  14. 14. C Species Information Page
  15. 15. Functionality of the Pytophthora Database Data Submission BLAST Search Virtual Gel Sequence Alignment Phylogenetic Tree Data Download & Storage Marker Sequences Database Cart & Folder
  16. 16. Functionality of the Pytophthora Database
  17. 17. On-going Work Linking isolate data from genome to ecosystem
  18. 18. Global Virtual Network of Plant Pathologists North America South America Africa Europe Asia GPN (V) GIS (III)Diagnostic Tools (I) Pathogen Database (II) Global Distribution A population B population A genotype B genotype (III) Diagnostic Tools A B C D DiagnosisCollection Isolation Oceania (IV) Analysis Tools P. infestans NI909 QUERY 1152 ML-91 8470 91T16 JP34 Py-D New Isolates Central America (VI) Human Resource Short-term visit Workshop Meetings International network Information for Education/Extension Cyberinfrastructure linking data, ‘e-tools’ and global human capital to support the management of new or reemerging pathogens.

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