2009 Spring Plant Pathology Seminar

1. Phytophthora and Pythium DatabasesPhytophthora and Pythium Databases
A growing cyberinfrastructure supporting the identificationA growing cyberinfrastructure supporting the identification
and monitoring of major pathogen groupsand monitoring of major pathogen groups
Bongsoo Park,
Department of Plant Pathology
The Pennsylvania State University

2. OutlineOutline
 Phytophthora & Pythium
 Database Issues in Biology
 Phytophthora Database
◦ Letter to Phytophthora Community
◦ Current needs and Problems
◦ Specific Objectives of the PD Project
◦ Functionality of the PD
◦ How can we use this database
 Pythium Database
 Future Directions
 Acknowledgements

3. Phytophthora & PythiumPhytophthora & Pythium
 Taxonomy
Eukaryota > Chromista (Kingdom)> Oomycota >
Oomycetes(Class)> Peronosporales > Pythiaceae > Phytophthora
Facultative parasites
Soil- and water-borne

4. Phytophthora & PythiumPhytophthora & Pythium
The genus Phytophthora is closely related to the genus Pythium.
Two genera listed in order of the dates of their descriptions :
Pythium Pringsheim (1858), Phytophthora de Bary (1876)
Nathanael Pringsheim (1823-1894)
http://www.deutsche-botanische-gesellschaft.de/
Heinrich Anton de Bary (1831-1888)
http://en.wikipedia.org/wiki/Heinrich_Anton_de_Bary

5. Sudden Oak Death (SOD) in CA and OR
Serious threat to the US forests
Phytophthora ramorum
Symptoms include bleeding cankers on the tree’s trunk and dieback of the
foliage.

6. Tanoak canker
Tip necrosis on Rhododendron leaves
Ivors, K. http://www.phytophthoradb.org/
Ivors, K. http://www.phytophthoradb.org/

7. Database: DefinitionDatabase: Definition
 Database: The collection of Data
 Database systems are designed to manage large bodies
of information.
 Management of data involves both
defining structures for stored information &
providing mechanisms for the management and utilization
of the information.
PD

8. Change in my perspectiveChange in my perspective
Phytophthora Database
Phytophthora Database

9. Plant Pathology Database(?)Plant Pathology Database(?)
 Pathogen Genome Sequences
 Plant Pathogen or Disease Images
 Host & Disease reports
 Book Chapters
(PD : Phytophthora Diseases Worldwide)
 Experimental Protocols
(http://openwetware.org)
 Expertise Human Resource
(http://www.apsnet.org,http://www.epernicus.com)
 Communication Repository (Forum,Blog, Twitter)

10. New Journal for DatabaseNew Journal for Database
 The 2009 issue of Nucleic Acid Research includes
descriptions of 179 databases, of which 95 are new.
 Nucleic Acids Research online Molecular Biology
Database Collection (Total 1170!)
(http://www.oxfordjournals.org/nar/database/a/)
Welcome to Database: The Journal of Biological
Databases and Curation
New Journal will be initiated in 2009

11. Genome Sequencing DatabaseGenome Sequencing Database
 Major Genome DBs: NCBI, EBI, DDJB
 Genomes OnLine Database
http://www.genomesonline.org/

12. Letter to Phytophthora CommunityLetter to Phytophthora Community
Phytopathology 2006, Volume 96, Number 9, Pages 920-925

13.  Global genotypic and phenotypic diversity of plant
pathogens and their distribution and dynamics need to be
analyzed and archived in a format that can be easily accessed
and visualized.
• Difficulties in identifying and tracking pathogens
• High degrees of pathogen diversity and dynamics in nature
Current Needs & ProblemsCurrent Needs & Problems

14.  Global genotypic and phenotypic diversity of plant
pathogens and their distribution and dynamics need to be
analyzed and archived in a format that can be easily accessed
and visualized.
• Difficulties in identifying and tracking pathogens
• High degrees of pathogen diversity and dynamics in nature
• Urgent need for global cooperation in dealing with disease
problems
• Properly archiving data is as important as generating new data!
Current Needs & ProblemsCurrent Needs & Problems

15.  Pathogen culture collections are invaluable assets
• Primary links to past disease epidemics and research
activities, including genomics
Current Needs & ProblemsCurrent Needs & Problems

16. 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.
Specific Objectives of the PD ProjectSpecific Objectives of the PD Project

17. 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.
Specific Objectives of the PD ProjectSpecific Objectives of the PD Project

18. Development of new phylogenetic markers based
on the genome sequences of P. ramorum, P. capsici, P. sojae
and P. infestans.
ProgressProgress

19. 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.
ProgressProgress

20. 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 identification of ~3,000 isolates (>90
species).
Establishment of the Phytophthora Database.
Characterization of individual species complexes
(e.g., P. cinnamomi, P. capsici)
ProgressProgress

21. Phytophthora
Database
The
number
Member 381
Country 41
Species Description 94
Pathogen Isolates 1,762
Genetic Marker Sequences 3,641
GlobalGlobal PhytophthoraPhytophthora NetworksNetworks

22. Phytophthora infestansPhytophthora infestans Genome DatabaseGenome Database

23. Phytophthora sojaePhytophthora sojae EST DatabaseEST Database
Starting with Phytophthora sojae, EST
sequences
http://vmd.vbi.vt.edu/EST/

24. PhytophthoraPhytophthora genus, Forensic Databasegenus, Forensic Database
http://www.phytophthoradb.org

25. Park et al. Plant Disease (2008) 92: 966-972
Phytophthora DatabasePhytophthora Database

26. 55
C
Phytophthora infestansPhytophthora infestans
Phytophthora Disease Worldwide
Donald C. Erwin
Olaf K. Ribeiro

27. Data Submission
BLAST Search
Virtual Gel
Sequence Alignment Phylogenetic Tree
Data Download & Storage
Marker Sequence
Database
Cart & Folder
Functionality of the PDFunctionality of the PD

28. The available programs in PDThe available programs in PD
BLAST Search ClustalW
Sequence
Alignment
Phyloviewer Virtual RFLP Cart & Folder
System
Ver 2.0
(Ver2.2 new)
Ver 1.7
(Ver2.0 new)
Ver 1.0 Ver 1.0 Ver 1.0
Basic
Local
Alignment
Search
Tool
Multiple
Sequence
Alignment
Program
Phylogenetic
Tree drawing
Program
Virtual Gel
Running
Program
Storaging Sharing
Tool
Myers, E.
Altschul S.F.
Gish W.
Miller E. W.
Lipman D. J.
Gibson T.
Thompson J.
Higgins D.
Park B.
Park J.
Park J. Park B.
Park J.
Since 1990 Since 1994 Since 2007 Since 2007 Since 2006

29. How can we use the database?How can we use the database?
 Database curation works
 GenBank vs PD
GenBank
2008
GenBank
2009
PD
2008
PD
2009

30. Datamining ofDatamining of PhytophthoraPhytophthora ITSITS
Species Apr. 20081
Jan. 20091
P. capsici 197 198
P. cactorum 164 177
P. cinnamomi 155 162
P. cryptogea 149 152
P. infestans 144 146
P. citricola 134 153
P. nicotianae 111 169
P. megasperma 92 95
P. citrophthora 83 83
P. ramorum 75 77
Phytophthora sp. 152 213
Other species 969 (90) 1,045(91)
Total number 2,425 2,670
NCBI Accession # Submitted identity Likely identity
AF228096 P. drechsleri P. cajani
AF228093 P. drechsleri P. melonis
AF228095 P. drechsleri P. melonis
AY251650 P. drechsleri P. melonis
AY251652 P. drechsleri P. cinnamomi
AY251651 P. drechsleri P. melonis
AY659656 P. cryptogea P. melonis
AY745754 P. nicotianae Not sure
DQ092419 P. alni Not sure
AB217679 P. megasperma Not sure
AB217685 P. sojae P. citricola
DQ831527 P. cinnamomi P. cryptogea
DQ821190 P. nicotianae P. cryptogea
EF173471 P. infestans Not sure
DQ501284 P.drechsleri P. melonis
DQ831524 P. megasperma P. medicanis
AB217680 P. megasperma Not sure
EF490382 P. citricola P. pseudosyringae
EU044732 P. citricola P. cactorum
EU194394 P. megasperma P. cryptogea
EF490383 P. pseudosyringae P. citricola
EU000073 P. cryptogea P. megasperma
EU194389 P. megasperma P. erythorosepica
AB367382 P. drechsleri P. niederhauserii
EQ490382 P. citricola P. pseudosyringae

31. How can we use the database?How can we use the database?
 Quality of PD will ensure much better search results,
and we will address the importance of community data
curation.
PD

32. How can we use the database?How can we use the database?
PD
 Phylogenetic tree will be updated and studied in
more systemic and organized manners.
Jamie E. Blair et al, Fungal Genetics & Biology

33. How can we use the database?How can we use the database?
 Phylogenetic tree will be updated and studied in more
systemic and organized manners. Phyloviewer program
will be updated and utilized in PD.
Phyloviewer program, created by B. Park. 2007

34. How can we use the databaseHow can we use the database
 RFLP Virtual Gel
 Cyber lab, it’s just first step.
Virtual RFLP program, created by J. Park. 2007

35. How can we use the database?How can we use the database?
 Presenting a standardized database schema to the global
plant pathology community
PD
Species Information
Isolate Information
Sequence Information
Being a standard database
Intensive collaboration will be possible.

36. Pythium DatabasePythium Database
http://www.pythiumdb.org

37. Future DirectionsFuture Directions
 Pythium Database working with
Dr. Moorman and others (http://www.pythiumdb.org)
 Fusarium Database working with
Dr. Geiser and others (http://isolate.fusariumdb.org)
 Being the standard of Plant Pathogen Isolate Databases
from Plant Saving University
 Working on GIS tools with ZedX
 Working on genomic browser and comparative
genomics tools in collaboration with Fungal
Bioinformatics Lab

38. Future DirectionsFuture Directions
Big pictures for
plant pathogen database
PD
Pythium
DB
Fusarium
DB

39. Future DirectionsFuture Directions
Integration all available tools and data
from genome to geospatial context
Dr. Kang’s proposal

40. AckledgementsAckledgements
Penn State
 Dr. Seogchan Kang
 Dr. David M. Geiser
 Dr. Gary W. Moorman
 Dr. Michele A. Mansfield
 Dr. Frederick Gildow
 Dr. Maria del Mar Jimenez-Gasco
 Dr. Beth K. Gugino
 Dr. Yong-Hwan Lee (Seoul National University, Korea)
 Dr. Jamie E. Blair (Franklin & Marchall College, PA)
 Dr. Kelly Ivors (North Carolina State University, NC)
 Dr. Mike Coffey (University of California in Riverside, CA)
 Dr. Frank Martin (USDA-ARS)
 Seogchan Kang’s Lab members in Penn State
 Fungal Bioinformatics Lab members in Seoul National Univ
 Department of Plant Pathology
 USDA Plant Biosecurity grant (2008-55605-18773)

41. Thank you.Thank you.
http://ppathblog.psu.edu