CPGR Overview

Transcript Assemblies(TAs):

Group Species
Fungi 58
Nematode 17
Oomycete 7
Total 82

For more information about the CPGR TAs, see the CPGR TA Overview

Genomes

rDNA Database

  • 65,232 Plant Pathogen rDNA Seqs
  • 3,760 Plant Pathogen Species

  • 66,523 Related rDNA Seqs
  • 13,853 Related Species

  • 131,755 Total rDNA Seq
  • 17,613 Total Species

Genome Warehouse

 Status
Group F D IP EST
Bacteria 34 15 14 0
Fungi 7 13 14 22
Nematode 0 2 0 14
Oomycete 0 6 0 6
Virus 623 0 0 0
Viroids 36 0 0 0
Total 700 36 28 42

Status: F - Finished, D - Draft, IP - In progress, EST - EST Project

CPGR News

Introduction to the Comprehensive Phytopathogen Genomics Resource

Welcome to the Comprehensive Phytopathogen Genomics Resource(CPGR). The CPGR aims to provide a comprehensive plant pathogen genomics and annotation resource. A major part of the CPGR is the development of diagnostic molecular markers and robust diagnostic protocols for plant pathogens. To keep informed of developments on the CPGR site, please sign up on the CPGR mailing list.

We have received funding from USDA NIFA to continue our work on the CPGR in collaboration with Nicole Perna, University of Wisconsin. Our focus will be on improving the value of plant pathogen genome sequences through uniform, updated and value-added annotation. We will merge our efforts with the CPGR which provides access to genome sequence and annotation for plant pathogens with the A Systematic Annotation Package (ASAP) project, which provides an environment for integration and curation of annotations derived from diverse sources. The objectives of this project are to 1) collate and update genome sequence and anntotation data for all plant pathogen taxa, 2) employ robust computational pipelines to provide updated, synchronized, and uniform structural and functional annotation of sequenced plant pathogen genomes, 3) provide comparative genomic analyses across genera to facilitate genome interpretation, and 4) manually curate known and putative virulence factors with supporting evidence in bacterial plant pathogen genomes. Through the use of Wikipedia pages that will be written by plant pathology graduate and undergraduate students, we will inform the general public of plant pathogens, the diseases they cause, and the information available through their genome sequence and annotation.

Comprehensive Plant Pathogen Genomic Warehouse

The Comprehensive Plant Pathogen Genomic Warehouse is a database of finished, draft and in progress genome sequencing projects and EST projects for viral, bacterial, oomycete, fungal, and nematode plant pathogens. It will be updated on a frequent basis and and will be integrated into the main CPGR annotation database and comparative analysis database serving as a portal for the database.

Plant Pathogen Ribosomal DNA (rDNA) Database

The CPGR Plant Pathogen Ribosomal DNA (rDNA) Database contains all the ribosomal DNA in GenBank for Bacterial, Oomycete, Nematode and Fungal plant pathogens. The rDNA sequences for other species in the genus of each pathogen are also stored in the database. The web interface for the rDNA database allows searching to find the genera and species of interest, selection between nuclear and mitochondrial rDNA for eukaryotes, display of the defintion lines of the rDNA sequences to allow fine control over selecting the sequences, and the choice displaying the sequence in the browser or sequence file download.

Plant Pathogen Transcript Assemblies

An objective of the CPGR is the clustering and assembling of ESTs generated from plant pathogen EST projects. For this project, we have developed an automated EST clustering and assembly pipeline based on the tgicl package. The clustering and assembly process forms sets of unique transcipts or transcript assemblies. Basic search, report, flat file data and a plant pathogen BLAST server are now available and we will implementing enhanced annotation of the transcript assemblies and search tools in the near future.

Maintenance Notice

We have planned server maintenance on the first Wednesday of every month. CPGR web pages may be unavailable or only partially functional during server maintenance

Work on the CPGR and ASAP is supported by grants to Robin Buell, Jan Leach, and Ned Tisserat from the USDA (CPGR: 2006-55605-16645, 2006-55605-04558) and to Robin Buell and Nicole Perna from the USDA (CPGR & ASAP 2009-65109-05719).

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