Global unique device identification database (gudid) and udi
Phytophthora identification with “The Phytophthora database”
Transcript of Phytophthora identification with “The Phytophthora database”
Phytophthora identification with “The Phytophthora database”
Dr. Kelly IvorsDept. Plant Pathology
North Carolina State UniversityMountain Hort. Crops Research & Extension Center
Mills River (Fletcher), NC
NC STATE Plant Pathology
Phytophthora DatabaseCyberinfrastructure 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
http://www.phytophthoradb.org
Principal InvestigatorsPenn State: Seogchan Kang, David Geiser & Izabela MakalowskaUC-Riverside: Mike CoffeyNorth Carolina State University: Kelly IvorsUSDA-ARS: Frank Martin & Kerry O’Donnell
USDA-NRI Plant Biosecurity
Our knowledge on the diversity and ecology of Phytophthora is limited.
The rapid expansion of global trade and human travel has greatly accelerated the
introduction of exotic pathogens and variants of endogenous pathogens.
Objectives of the Project
To establish a comprehensive phylogeneticframework for the genus Phytophthora
To build an internet database that To build an internet database that crosslinkscrosslinksthe genotype, phenotype, and distribution of the genotype, phenotype, and distribution of individual individual PhytophthoraPhytophthora species/isolates (generate species/isolates (generate data for database)data for database)
To develop and optimize molecular diagnostic To develop and optimize molecular diagnostic tools for detecting and identifying tools for detecting and identifying PhytophthoraPhytophthora
Park, J., Ivors, K., Kang, S. et al. 2008. Phytophthora Database: A forensic database supporting the identification and monitoring of Phytophthora. Plant Dis. 92:966-972.
Park et al. Plant Disease (2008) 92: 966-972
www.
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Organization of the Pytophthora Database
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Functionality of the Pytophthora Database
Data Submission
BLAST Search
Virtual Gel
Sequence Alignment Phylogenetic Tree
Data Download & Storage
Marker SequenceDatabase
Cart & Folder
Functionality of the Pytophthora Database
Global Global PhytophthoraPhytophthora NetworkNetwork
PhytophthoraDatabase
CurrentStatistics
Registered Users >400Countries ~50
Species Covered 106Isolates Archived 2,356Genetic Marker
Sequences4,651
Global Global PhytophthoraPhytophthora NetworkNetwork
Identification of ~2,600 isolates from multiple labs by sequencing the ITS region:
1.PA Dept. of Agriculture (~700)2.UC-Riverside (~1,000)3.Clemson University (~300)4.University of Maryland (~200)5.Chongbook National University in Korea (~150)6.NC State (~100)7.Ohio State University (~100)8.Inst. for Plant Protection in Germany (~50)
Identification of ~2,600 isolates from multiple labs by sequencing the ITS region:
1.PA Dept. of Agriculture (~700)2.UC-Riverside (~1,000)3.Clemson University (~300)4.University of Maryland (~200)5.Chongbook National University in Korea (~150)6.NC State (~100)7.Ohio State University (~100)8.Inst. for Plant Protection in Germany (~50)
Global Global PhytophthoraPhytophthora NetworkNetwork
In Depth Phylogenetic Analysis & New Species Description:
1.Analysis of P. capsici and P. cinnamomi species complexes using 7 nuclear and 4 mitochondrial loci2.New species description in collaboration with Yilmaz Balci (UMD), Mike Coffey (UC-Riverside), and Seong H. Kim (PDA)
In Depth Phylogenetic Analysis & New Species Description:
1.Analysis of P. capsici and P. cinnamomi species complexes using 7 nuclear and 4 mitochondrial loci2.New species description in collaboration with Yilmaz Balci (UMD), Mike Coffey (UC-Riverside), and Seong H. Kim (PDA)
Five ProteinFive Protein--coding Loci:coding Loci:-- 60S Ribosomal Protein L10 60S Ribosomal Protein L10 -- BetaBeta--tubulintubulin-- EnolaseEnolase-- Heat Shock Protein 90Heat Shock Protein 90-- Elongation Factor 1 alphaElongation Factor 1 alpha-- rRNArRNA Large SubunitLarge Subunit
Ppseudotsugae Pcactorum
Pnicotianae Pphaseoli
Pipomoeae Pinfestans
Pquercina Pbisheriae
Pmultivesiculata Pcitricola Pspecies 22
Pbotryosa Pinflata
Ptropicalis Pmexicana Pcapsici
Pmegakarya Peronophythora litchii
Ppalmivora Parecae
Pheveae Pkatsurae
Pinundata Phumicola
Pgonapodyides Pmegasperma
Pasparagi Pnemorosa Pilicis Ppsychrophila
Pcambivora Palni Pfragariae
Puliginosa Pcinnamomi Psinensis
Psojae genome Prichardiae Perythroseptica Pcryptogea
Pkelmania Pdrechsleri
Pmedicaginis Pfoliorum Pramorum genome Pramorum
Psyringae Phibernalis
Pprimulae Pporri
Pbrassicae Pythium vexans
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0.01
Clade 1
Clade 2
Clade 4Clade 5
Clade 3?
Clade 6
Clade 7
Clade 8
PhylogeneticPhylogenetic RelationshipsRelationshipsAmong Among PhytophthoraPhytophthora
Blair Blair et alet al. 2008. 2008www.phytophthoradb.orgwww.phytophthoradb.org
Global Global PhytophthoraPhytophthora NetworkNetwork
Fighting Phytophthara: A Workshop during the 2008 APS Meeting
1. 90 registered attendants and 9 speakers2. A protocol book resulted from this workshop will be published by the APS Press.
Fighting Phytophthara: A Workshop during the 2008 APS Meeting
1. 90 registered attendants and 9 speakers2. A protocol book resulted from this workshop will be published by the APS Press.
Proposal submitted to APSand accepted
On-line information delivery?
Molecular Technology for Phytophthora identification and Development of Diagnostic Markers
Molecular Technology for Phytophthora identification and Development of Diagnostic Markers
Species-Specific Diagnostic MarkersSpecies-Specific Diagnostic Markers
Detailed Description of Diagnostic MarkersDetailed Description of Diagnostic Markers
Sequence Alignment Files for DownloadingSequence Alignment Files for Downloading
Reference Management SystemReference Management System
Geographic Information Systems Tools
Geographic Information Systems Tools
On-going WorkViewing isolate data from genome to ecosystem
On-going WorkViewing isolate data from genome to ecosystem
Future DirectionFuture DirectionCyberCyber--infrastructure for infrastructure for PhytophthoraPhytophthora
PhytophthoraPhytophthoraDatabase (PD)Database (PD)
http://http://www.phytophthoradb.owww.phytophthoradb.orgrg//
PhytophthoraPhytophthoraHuman NetworkHuman Network