|Grunwald, Niklaus - Nik|
|Luster, Douglas - Doug|
Submitted to: Plant Disease
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/5/2008
Publication Date: 6/5/2008
Citation: Park, J., Park, B., Veeraraghavan, N., Jung, K., Lee, Y., Blair, J.E., Geiser, D., Isard, S., Mansfield, M.A., Nikolaeva, E., Park, S., Kim, S.H., Greene, M., Ivors, K.L., Balci, Y., Peiman, M., Erwin, D.C., Coffey, M.D., Rossman, A.Y., Farr, D.F., Cline, E., Grunwald, N.J., Luster, D.G., Schrandt, J.K., Martin, F.N., Ribeiro, O.K., Makalowska, I., Kang, S. 2008. Phytophthora Database: A forensic database supporting the identification and monitoring of Phytophthora. Plant Disease. 92:966-972. Interpretive Summary: Fungi and fungal-like organisms cause billions of dollars damage each year to U.S. agriculture and forestry. Most recently, a newly discovered fungal-like organism in the genus Phytophthora was discovered to cause a disease called Sudden Oak Death that has killed numerous forest trees in the western U.S. A related species in this genus was the cause of potato late blight, the organisms that lead to the Irish potato famine in the 1840’s when over one million people immigrated to the U.S. Despite their importance, information about these organisms is often difficult to obtain. This paper reports on a newly developed bioinformatics system in which all data about species in the genus Phytophthora are synthesized into one easily accessible system. The system includes information on the scientific name, where the organism occurs, and how to identify each species using methods based on looking at its microscopic structures and sequencing a unique gene characteristic of each species. This system will allow scientists and policy makers to quickly respond to problems caused by these organisms such as the identification of the species and determining plant quarantine policies based on what plants may harbor species that do not occur in the U.S.
Technical Abstract: Due to their high virulence and ability to spread rapidly, Phytophthora species represent a serious threat to agricultural production and ecological systems. Many novel Phytophthora species have been reported in recent years, indicative of our limited understanding of the ecology and diversity of Phytophthora in nature. Systematic cataloging of genotypes and phenotypes of cultures preserved in historical collections can serve as a baseline for accurate identification, classification, and risk assessment of new Phytophthora isolates in future surveys. The Phytophthora Database (PD) catalogs such data in a web-accessible format that can be easily searched, updated, and shared. Data search/analysis tools were incorporated to facilitate uses of PD, which include (i) BLAST to allow for identification of an unknown isolate to the closest species or population by querying the database, (ii) a program for building phylogenetic trees to visualize evolutionary relationships among selected isolates, and (iii) a virtual gel for RFLP analysis. The PD also provides a means of storing and sharing data for individual users, thus allowing customized uses of PD and facilitating collaboration among users. Additional tools are currently being developed to expand its functionality. The PD can be easily adopted to build databases for other pathogen groups.