Location: Systematic Mycology and Microbiology
2008 Annual Report
Objective 2. On-line database resources about fungi developed at the SMML will continue to be updated and increased as new specimens are accessioned and new data are published. As funding permits, the nomenclature file will be updated. Additions to the on-line identification systems are made as additional taxa are studied and described by the associated scientists. As unique sequences, i.e. DNA barcodes, are developed for these species, there will be a link to these GenBank sequences. Descriptions and illustrations of invasive fungi will be placed on the Internet as they become available. New software will be evaluated especially Adobe Flex software to facilitate the ability to work efficiently with these databases. Computer programs and operating system software and hardware will be continually under review and incorporated as deemed necessary and useful.
This past year the major activity of the scientist and collections manager concerned the rewriting of the data entry screens and conversion of the fungal databases in a new version using MySQL, Flex, and ColdFusion for Web applications. An outside contractor was hired to assist with this in order to develop standardized, user-friendly data entry screens that can be accessed remotely. This basic work is nearly completed, although a second activity has been initiated of developing programs to make appropriate research data available on the Web.
This work relates to National Program 301 Plant Genetic Resources, Genomics, and Genetic Improvement, Component I. Plant and Microbial Genetic Resource Management, Efficiently and Effectively Manage Plant, and Microbial Genetic Resources.
Recently, a newly discovered fungal-like organism in the genus Phytophthora was discovered to cause a disease called Sudden Oak Death that has killed many forest trees in the western U.S. A related species in this genus was the cause of potato late blight, the disease 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 research provides a summary of reports about all species of Phytophthora including a bioinformatics system that synthesizes data about these species into one easily accessible system. The system includes information about 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 for each species. About half of the species of Phytophthora known worldwide do not occur in the U.S. This research allows scientists and policy makers to determine plant quarantine policies based on what plants may harbor species of Phytophthora not in the U.S. The research contributes to National Program 303, Plant Diseases, Component 1, Detection, Identification, Characterization, and Classification of Pathogens.
5.Significant Activities that Support Special Target Populations
Cline, E., Farr, D.F., Rossman, A.Y. 2008. A synopsis of Phytophthora with accurate scientific names, host range, and geographic distribution. Plant Health Progress. http:dx.doi.org/10.1094/PHP-2008-0318-01-RS. http://www.plantmanagementnetwork.org/sub/php/review/2008/phytophthora/
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.