CPGR Overview
Transcript Assemblies(TAs):
| Group | Species | TAs |
|---|---|---|
| Fungi | 37 | 210,718 |
| Nematode | 15 | 66,891 |
| Stramenopile | 5 | 69,353 |
| Total | 57 | 346,962 |
For more information about the CPGR TAs, see the CPGR TA Overview
Genomes
rDNA Database
- 22,099 Plant Pathogen rDNA seqs
- 48,840 related rDNA seqs
Genome Warehouse
| Status | ||||
|---|---|---|---|---|
| Group | F | D | IP | EST |
| Bacteria | 28 | 10 | 17 | 0 |
| Fungi | 5 | 10 | 11 | 19 |
| Nematode | 0 | 1 | 0 | 14 |
| Stramenopile | 0 | 4 | 2 | 5 |
| Virus | 623 | 0 | 0 | 0 |
| Viroids | 36 | 0 | 0 | 0 |
| Total | 692 | 25 | 20 | 38 |
Status: F - Finished, D - Draft, IP - In progress, EST - EST Project
CPGR News
- CPGR Workshop at the APS Meeting, Jul 2008 - Workshop Slides Available
- CPGR Warehouse Updated - April 2008 - 4 new finished genomes
- CPGR Warehouse Updated - March 2008
- The CPGR Transcript Assemblies have been updated: 8 new species added, 4 existing TAs updated.
- Sign up for CPGR mailing list to recieve updates by email
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.
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, stramenopile, 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, Stramenopile, 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.
Under Development
CPGR web site: The Genomes section is being completed, and new pages are being added daily.
Diagnostics: Work on the Xanthomonas Oryzae pathovars is being completed and will be available soon. Work on Pythium diagnostic markers is starting soon.
