The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

Ned Tisserat,Bishwo N Adhikari,C André Lévesque,C Robin Buell,Eric C Neeno-Eckwall,Jan E Leach,John P Hamilton,Nicole T Perna

doi:10.1093/database/bar053

Abstract

The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera.Database URL: http://cpgr.plantbiology.msu.edu.

Highlights

The genomes of plant pathogens range from small nucleic acid molecules in viruses and viroids, typically in the kilobase size range or smaller, to large, complex genomes in the megabase (Mb) range in higher eukaryotic pathogens including fungi, oomycetes and nematodes
The genomics era for cellular plant pathogens began in 1999 with the publication of Expressed Sequence Tags (ESTs) from Phytophthora infestans [1], which are single pass sequences of cDNAs that are highly informative with respect to gene discovery and assessment of expression levels
We have created a ‘Genome Warehouse’ that is a webbased information portal for plant pathogens in which genome or large-scale transcriptome sequence data sets for viroids, viruses, oomycetes, nematodes, fungi and bacteria are collated to provide the community with the status, source and metadata regarding each genome project

Summary

Introduction

The genomes of plant pathogens range from small nucleic acid molecules in viruses and viroids, typically in the kilobase (kb) size range or smaller, to large, complex genomes in the megabase (Mb) range in higher eukaryotic pathogens including fungi, oomycetes and nematodes. Due to their smaller size, genome sequences for viruses and viroids can be determined using conventional molecular biology and first-generation sequencing methods such as Sanger sequencing. An EST collection typically contains redundant, as well as partial sequences of the same transcript (mRNA) concomitant with sequencing errors due to the single pass nature of the method. EST approaches for gene discovery are well established in phytopathological research; these approaches have yielded new information on pathogenesis [5,6,7,8,9]

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Conclusion