The National Center for Genome Resources (NCGR), Santa Fe, NM, in partnership with investigators at the Ohio State University, the Joint Genome Institute (JGI) of the Department of Energy, and the University of Tennessee will obtain DNA sequence for the entire genome of Phytophthora capsici. This project will provide a comprehensive sequence of the genome of Phytophthora capsici using a novel technology developed by 454 LifeSciences. The technology greatly accelerates genome sequencing, making it possible to not only sequence the entire genome of a single strain of this vegetable pathogen, but to also sequence the genome of multiple strains that infect different vegetable crops and differ in virulence and resistance to antifungals. The collaborators will provide sequence information using the world-wide-web through the Phytophthora Functional Genomic Database (PFGD; www.pfgd.org).
Phytophthora capsici is a devastating pathogen of vegetable crops such as cucurbits (squashes, pumpkins, etc.), tomatoes, and peppers. First reported in the US in 1922 on chili peppers in New Mexico, Phytophthora capsici has spread widely to become a pathogen of national economic importance. It has also broadened its host range recently to include legumes, such as snap and lima beans. Sequencing the genome of Phytophthora capsici will provide the critical knowledge and tools needed for comprehensive functional genomic studies to discover the genes that cause virulent outbreaks and that determine host range. In turn, these studies will help farmers, breeders and producers nationwide by development of improved diagnostics, resistant plant varieties, and better control measures.
This project brings together biotechnologists, software engineers and biologists from throughout the United States to address an increasing threat to vegetable and legume productivity by developing a tractable model for molecular dissection of Phytophthora evolution, adaptation and virulence. The approach has potential to impact all future genome sequencing efforts and will provide an opportunity to benchmark an important sequencing technology platform. Because NCGR is located in the only minority-majority state and provides internships targeted to Hispanic and Native Americans, this project will provide opportunities in bioinformatics, computational biology, biotechnology and genomics to individuals from groups that are largely underrepresented in these scientific disciplines.
This project is being supported through a collaboration of the National Science Foundation and the National Research Initiative of the Cooperative Research, Education, and Extension Service of the Department of Agriculture.
