Plant Pathology Seminar

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

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

Phytophthora & PythiumPhytophthora & Pythium Taxonomy

Eukaryota > Chromista (Kingdom)> Oomycota >

Oomycetes(Class)> Peronosporales > Pythiaceae > Phytophthora

Facultative parasitesSoil- and water-borne

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

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.

Tanoak cankerTip necrosis on Rhododendron leaves

Ivors, K. http://www.phytophthoradb.org/

Ivors, K. http://www.phytophthoradb.org/

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

Change in my perspectiveChange in my perspective

Phytophthora

Database

Phytophthora Database

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)

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

Genome Sequencing Genome Sequencing DatabaseDatabase Major Genome DBs: NCBI, EBI, DDJB

Genomes OnLine Database

http://www.genomesonline.org/

Letter to Phytophthora Letter to Phytophthora CommunityCommunity

Phytopathology 2006, Volume 96, Number 9, Pages 920-925

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

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

Pathogen culture collections are invaluable assets

• Primary links to past disease epidemics and research activities, including genomics

Current Needs & ProblemsCurrent Needs & Problems

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

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

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

ProgresProgresss

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

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

PhytophthoraDatabase

The number

Member 381

Country 41

Species Description 94

Pathogen Isolates 1,762

Genetic Marker Sequences

3,641

Global Global PhytophthoraPhytophthora Networks Networks

Phytophthora infestans Phytophthora infestans Genome Genome DatabaseDatabase

Phytophthora sojae Phytophthora sojae EST EST DatabaseDatabase

Starting with Phytophthora sojae, EST sequences

http://vmd.vbi.vt.edu/EST/

PhytophthoraPhytophthora genus, Forensic genus, Forensic DatabaseDatabase

http://www.phytophthoradb.org

Park et al. Plant Disease (2008) 92: 966-972

Phytophthora DatabasePhytophthora Database

55

C

Phytophthora infestansPhytophthora infestans

Phytophthora Disease Worldwide

Donald C. ErwinOlaf K. Ribeiro

Data Submission

BLAST Search

Virtual Gel

Sequence Alignment Phylogenetic Tree

Data Download & Storage

Marker SequenceDatabase

Cart & Folder

Functionality of the PDFunctionality of the PD

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

How can we use the How can we use the database?database?Database curation worksGenBank vs PD

GenBank 2008

GenBank 2009

PD2008

PD2009

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

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

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

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

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

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.

Pythium DatabasePythium Database

http://www.pythiumdb.org

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

Future DirectionsFuture Directions

Big pictures for plant pathogen database

PD

Pythium DB

FusariumDB

Future DirectionsFuture Directions

Integration all available tools and data from genome to geospatial

contextDr. Kang’s proposal

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)

Thank you.Thank you.

http://ppathblog.psu.edu