Project Summary
A clear need in U.S. agriculture is the identification and
discrimination of plant pathogens in the environment or in plant
material, thus facilitating a rapid response that could lead to
containment or elimination of the pathogen. However, robust and
inexpensive tools to initially identify and classify plant pathogens
are not available for the vast majority of plant pathogens. One
approach to expand our knowledge and development of applicable tools
for diagnostics is to utilize genomics. While genomic data is a
powerful resource for the development of diagnostic markers for plant
pathogens, its use is limited by the disparate nature of the data and
the lack of the requisite expertise of field/extension plant
pathologists to access, apply, and implement this data readily into
existing diagnostic programs. Our project would address these two
limitations by constructing a comprehensive resource that will house
all publicly available genome sequence and annotation data for plant
pathogens including viruses, bacteria, fungi, oomycetes, and nematodes
and contain a range of access and search tools to facilitate the use of
genomic data by the target community-plant pathologists and
diagnosticians. This database and resource will be coupled to:
An experimental component in which we develop genomic based
diagnostic
tools
An educational component involving training of extension
plant
pathologists and diagnosticians in genomics, bioinformatics, and
molecular diagnostic methods.
This project addresses the goal of enhancing the protection and safety
of the nation's agriculture and food supply through implementation of
genomic methodologies into diagnostics for plant pathogens.
CPGR Website Features
Comprehensive Plant Pathogen Genome Warehouse:
The CPGR
Genome Warehouse is a database of finished, draft and in progress
genome sequencing projects and EST projects for viral, bacterial,
stramenopile, fungal, and nematode plant pathogens.
Plant Pathogen
Transcript Assemblies: The CPGR Transcript Assemblies
database contains
the clustered and assembled ESTs from plant [ahtogen EST projects. The
clustering and assembly process forms sets of unique transcipts or
transcript assemblies.
Plant Pathogen Ribosomal DNA (rDNA) Database:
CPGR Plant Pathogen Ribosomal DNA (rDNA) Database contains all the
ribosomal DNA in GenBank for Bacterial, Stramenopile, Nematode and
Fungal plant pathogens. The rDNA sequences for other species in the
genus of each pathogen are also stored in the database.
Plant
Pathogen Genome Tools: Tools to search and examine the
annotation of
the sequenced plant pathogens in GenBank.
Plant Pathogen Genome
Browser: The Genome Browser for viewing the annotation and its genomic
context in a graphical format.
SSR Candidate Marker Search Tool: The
SSR Candidate Marker Search Tool finds SSRs in a query sequence and
generates primers flanking the SSRs using primer3.
BLAST Server: The
CPGR TA database and a database of all the plant pathogen sequences in
GenBank can be searched using our BLAST server.
Project Directors
C. Robin Buell, PhD, Michigan State
University
Jan Leach, PhD, Colorado State University
André Lévesque, PhD, Agriculture and
Agri-Food
Canada
Tom Powers, PhD, University of Nebraska
Ned Tisserat, PhD, Colorado State University
Website and E-mail Contact
CPGR Website: (http://cpgr.plantbiology.msu.edu/)
CPGR Email:
CPGR
at plantbiology.msu.edu
