Progress 03/01/07 to 02/28/08
Outputs
OUTPUTS: We have disseminated a large amount of data to the public through our project web pages (http://cpgr.tigr.org to be moved in early February 2008 to http://cpgr.plantbiology.msu.edu). On these web pages, the genome warehouse, transcript assemblies, ribosomal DNA database, and other search/analysis tools/resources are available for public use. All data is also available for anonymous FTP download. All sequences are available for BLAST searching as well. We have released ~9,500 Expressed Sequence Tags for Pythium ultimum to the public dbEST database at Genbank. Work on the diagnostic component of the project is available through the project web pages and through presentations by project personnel at scientific meetings. We have disseminated our knowledge on genomics, bioinformatics, and genomics-based diagnostic marker development through two workshops for diagnosticians and plant pathologists. The lectures and presentation materials for these two workshops are available
through the project web pages.
PARTICIPANTS: Individuals PD: C. Robin Buell, J Craig Venter Institute (as of 10/1/07 Michigan State University), performed oversight and management to the project. coPD: Jan Leach, Colorado State University, performed oversight and management for the project. Bioinformaticist: John Hamilton, J Craig Venter Institute (as of 10/1/07 Michigan State University), performed bioinformatics support to the project. Research Associate: Jillian Lang, Colorado State University, performed experimental work on the project with respect to testing new diagnostic markers for plant pathogens. Partners: J Craig Venter Institute, Rockville, MD; Michigan State University, East Lansing MI; Colorado State University, Ft Collins, CO; Agriculture and Agri-Food Canada; University of Nebraska, Lincoln; Collaborators: Dr.Congfeng Song, Dept. Plant Pathology, Nanjing Agricultural University, Nanjing, 210095; Dr. Casiana Vera Cruz, International Rice Research Institute, Philippines; Dr. Valerie Verdier, INRA,
France; Dr. MarieAnne VanSluys, University of SaoPalo, Brazil; Training We have disseminated our knowledge on genomics, bioinformatics, and genomics-based diagnostic marker development through workshops for diagnosticians and plant pathologists. The lectures and presentation materials for these workshops are available through the project web pages.
TARGET AUDIENCES: The target audience is diagnosticians, plant pathologists, molecular biologists, genomicists, microbiologists, and bioinformaticists.
Impacts
We have been able to summarize for the scientific community the extent of genomic sequence available for plant pathogens. Prior to our project, it was impossible to find the number or status of genome sequencing/annotation projects for plant pathogens. Through our centralization of data and information, we have enabled the scientific community. We have made available to the scientific community so that they can more readily data-mine the genome sequences and annotation that are available. This has enabled a number of scientists in their individual research program. With respect to monitoring of access to the webpages (which would reflect use), since the pages were deployed in March, 2006, we have had a total of 2460 unique visitors with 67,195 access hits since the beginning of the project (through August 31, 2007). We are continuing to expand the content and tools available on the project web pages and will further expand the pages through the course of the project.
With respect to the diagnostic component of the project, we are in the final stages of developing a genomic-based diagnostic marker to distinguish Xanthomonas oryzae pv oryzae from Xanthomonas oryzae pv oryzicola. We have had numerous requests for these primer pairs and have provided this to researchers upon request. We have designed the first set of primers from Pythium transcripts to develop a species-specific diagnostic marker for Pythium and performed an initial round of amplifications. From this work, we have decided to expand our primer design and include genome-derived sequences in addition to transcript-derived sequences.
Publications
- No publications reported this period
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