Improving the Value of Plant Pathogen Genome Sequences Through Uniform, Updated and Value-Added Annotation

The genomics era has evolved such that the technologies and costs for obtaining genome sequence are well understood and feasible to achieve (to a large extent) depending on genome size and community engagement. The greater challenge, well acknowledged in both the bioinformatics and general research community, is accurate, informative annotation of genome sequences. Without dedicated efforts to update and improve annotation of plant pathogen genomes in a systematic manner, researchers will be handicapped by the “state-of-the-art” annotation available at the moment in time at which the genome was annotated. In the Comprehensive Phytopathogen Genome Resource project we employ comparative genomics, computational pipelines, and targeted manual curation to improve the annotation of plant pathogen genomes. Components of the project include: 1) updating and maintaining the Comprehensive Phytopathogen Genome Resource (CPGR) to include all newly released plant pathogen genomes and transcriptomes, 2) providing uniform and integrated functional annotation data for all CPGR gene and transcript sequences, 3) providing manually curated lists of known and putative virulence factors as well as supporting evidence through efforts of both a designated curator and the greater research community, 4) providing high quality comparative genomic data through OrthoMCL-based analyses and multiple genome alignments within genera, 5) providing genomic resources for diagnostic marker development, and 6) providing these resources to the research community through web-interfaces, download files, and search/analysis tools.