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VMD: a community annotation database for oomycetes and microbial genomes.
Sucheta Tripathy1, Varun N Pandey, Bing Fang
1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA-24061, USA.
Nucleic Acids Research
|December 31, 2005
Summary
The VBI Microbial Database now hosts genome sequences and annotations for plant pathogens Phytophthora sojae and Phytophthora ramorum, aiding research. This resource provides valuable data for understanding these important agricultural threats.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Plant pathogens Phytophthora sojae and Phytophthora ramorum pose significant threats to agriculture.
- Publicly accessible, high-quality genome data is crucial for studying these organisms.
Purpose of the Study:
- To establish a centralized, publicly accessible database for microbial genome sequences.
- To provide comprehensive genome data and annotation for Phytophthora sojae and Phytophthora ramorum.
Main Methods:
- Genome sequencing and annotation were performed in collaboration with the DOE Joint Genome Institute.
- Gene models were validated using Fickett's and log-likelihood statistical methods.
- Functional annotation was achieved through BlastX and InterProScan analyses.
Main Results:
- The VBI Microbial Database (VMD) contains genome sequences (95 MB for P. sojae, 65 MB for P. ramorum) with approximately 19,000 and 16,000 gene models, respectively.
- Putative functions were assigned to 17,694 P. sojae and 14,700 P. ramorum genes.
- An interactive genome browser and community annotation interface were developed.
Conclusions:
- The VMD provides a valuable, user-friendly resource for researchers studying Phytophthora pathogens.
- Public access to curated genome data facilitates advancements in plant pathology and disease management.
- Community involvement in annotation enhances the database's utility and accuracy.