CPGR Overview

Transcript Assemblies(TAs):

Group Species TAs
Fungi 39 249,893
Nematode 15 70,602
Stramenopile 7 115,866
Total 61 436,361

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 32 12 19 0
Fungi 7 13 14 22
Nematode 0 2 0 14
Stramenopile 0 6 0 6
Virus 623 0 0 0
Viroids 36 0 0 0
Total 698 33 33 42

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

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.

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