plant pathology seminar
DESCRIPTION
2009 Spring Plant Pathology SeminarTRANSCRIPT
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Phytophthora and Pythium DatabasesPhytophthora and Pythium DatabasesA growing cyberinfrastructure supporting the A growing cyberinfrastructure supporting the identification and monitoring of major identification and monitoring of major pathogen groupspathogen groups
Bongsoo Park, Department of Plant PathologyThe Pennsylvania State University
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OutlineOutlinePhytophthora & PythiumDatabase Issues in BiologyPhytophthora 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 DatabaseFuture DirectionsAcknowledgements
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Phytophthora & PythiumPhytophthora & Pythium Taxonomy
Eukaryota > Chromista (Kingdom)> Oomycota >
Oomycetes(Class)> Peronosporales > Pythiaceae > Phytophthora
Facultative parasitesSoil- and water-borne
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Phytophthora & PythiumPhytophthora & PythiumThe 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
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Sudden Oak Death (SOD) in CA and OR Serious threat to the US forests
Phytophthora ramorumSymptoms include bleeding cankers on the tree’s trunk and dieback of the foliage.
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Tanoak cankerTip necrosis on Rhododendron leaves
Ivors, K. http://www.phytophthoradb.org/
Ivors, K. http://www.phytophthoradb.org/
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Database: DefinitionDatabase: Definition
Database: The collection of DataDatabase 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
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Change in my perspectiveChange in my perspective
Phytophthora
Database
Phytophthora Database
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Plant Pathology Plant Pathology Database(?)Database(?)Pathogen Genome SequencesPlant Pathogen or Disease ImagesHost & Disease reportsBook 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)
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New Journal for DatabaseNew Journal for DatabaseThe 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 CurationNew Journal will be initiated in 2009
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Genome Sequencing Genome Sequencing DatabaseDatabase Major Genome DBs: NCBI, EBI, DDJB
Genomes OnLine Database
http://www.genomesonline.org/
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Letter to Phytophthora Letter to Phytophthora CommunityCommunity
Phytopathology 2006, Volume 96, Number 9, Pages 920-925
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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
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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
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Pathogen culture collections are invaluable assets
• Primary links to past disease epidemics and research activities, including genomics
Current Needs & ProblemsCurrent Needs & Problems
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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 Specific Objectives of the PD ProjectProject
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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 Specific Objectives of the PD ProjectProject
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Development of new phylogenetic markers based on the genome sequences of P. ramorum, P. capsici, P. sojae and P. infestans.
ProgresProgresss
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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.
ProgresProgresss
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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)
ProgresProgresss
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PhytophthoraDatabase
The number
Member 381
Country 41
Species Description 94
Pathogen Isolates 1,762
Genetic Marker Sequences
3,641
Global Global PhytophthoraPhytophthora Networks Networks
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Phytophthora infestans Phytophthora infestans Genome Genome DatabaseDatabase
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Phytophthora sojae Phytophthora sojae EST EST DatabaseDatabase
Starting with Phytophthora sojae, EST sequences
http://vmd.vbi.vt.edu/EST/
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PhytophthoraPhytophthora genus, Forensic genus, Forensic DatabaseDatabase
http://www.phytophthoradb.org
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Park et al. Plant Disease (2008) 92: 966-972
Phytophthora DatabasePhytophthora Database
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55
C
Phytophthora infestansPhytophthora infestans
Phytophthora Disease Worldwide
Donald C. ErwinOlaf K. Ribeiro
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Data Submission
BLAST Search
Virtual Gel
Sequence Alignment Phylogenetic Tree
Data Download & Storage
Marker SequenceDatabase
Cart & Folder
Functionality of the PDFunctionality of the PD
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The available programs in The available programs in PDPD
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
BasicLocal AlignmentSearchTool
MultipleSequenceAlignmentProgram
PhylogeneticTree drawingProgram
Virtual GelRunning 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
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How can we use the How can we use the database?database?Database curation worksGenBank vs PD
GenBank 2008
GenBank 2009
PD2008
PD2009
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Datamining of Datamining of PhytophthoraPhytophthora ITS ITS Species Apr. 20081 Jan. 20091
P. capsici 197 198P. cactorum 164 177P. cinnamomi 155 162P. cryptogea 149 152P. infestans 144 146P. citricola 134 153P. nicotianae 111 169P. megasperma 92 95P. citrophthora 83 83P. ramorum 75 77Phytophthora sp. 152 213Other species 969 (90) 1,045(91)Total number 2,425 2,670
NCBI Accession # Submitted identity Likely identityAF228096 P. drechsleri P. cajaniAF228093 P. drechsleri P. melonisAF228095 P. drechsleri P. melonisAY251650 P. drechsleri P. melonisAY251652 P. drechsleri P. cinnamomiAY251651 P. drechsleri P. melonisAY659656 P. cryptogea P. melonisAY745754 P. nicotianae Not sureDQ092419 P. alni Not sureAB217679 P. megasperma Not sureAB217685 P. sojae P. citricolaDQ831527 P. cinnamomi P. cryptogeaDQ821190 P. nicotianae P. cryptogeaEF173471 P. infestans Not sureDQ501284 P.drechsleri P. melonisDQ831524 P. megasperma P. medicanisAB217680 P. megasperma Not sureEF490382 P. citricola P. pseudosyringaeEU044732 P. citricola P. cactorumEU194394 P. megasperma P. cryptogeaEF490383 P. pseudosyringae P. citricolaEU000073 P. cryptogea P. megaspermaEU194389 P. megasperma P. erythorosepicaAB367382 P. drechsleri P. niederhauseriiEQ490382 P. citricola P. pseudosyringae
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How can we use the How can we use the database?database?Quality of PD will ensure much better search
results, and we will address the importance of community data curation.
PD
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How can we use the How can we use the database?database?
PD
Phylogenetic tree will be updated and studied in more systemic and organized manners.
Jamie E. Blair et al, Fungal Genetics & Biology
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How can we use the How can we use the database?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
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How can we use the How can we use the databasedatabase
RFLP Virtual GelCyber lab, it’s just first step.
Virtual RFLP program, created by J. Park. 2007
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How can we use the How can we use the database?database?Presenting a standardized database schema
to the global plant pathology community
PD
Species InformationIsolate Information Sequence Information Being a standard database Intensive collaboration will be possible.
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Pythium DatabasePythium Database
http://www.pythiumdb.org
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Future DirectionsFuture DirectionsPythium 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 UniversityWorking on GIS tools with ZedXWorking on genomic browser and
comparative genomics tools in collaboration with Fungal Bioinformatics Lab
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Future DirectionsFuture Directions
Big pictures for plant pathogen database
PD
Pythium DB
FusariumDB
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Future DirectionsFuture Directions
Integration all available tools and data from genome to geospatial
contextDr. Kang’s proposal
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AckledgementsAckledgementsPenn 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)
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Thank you.Thank you.
http://ppathblog.psu.edu