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United States Department of Agriculture

Agricultural Research Service

Research Project: THE U.S. NATIONAL FUNGUS COLLECTIONS AND DEVELOPMENT OF ON-LINE RESOURCES ABOUT FUNGI

Location: Systematic Mycology and Microbiology

2008 Annual Report


1a.Objectives (from AD-416)
Objective 1. Curate specimens in the U.S. National Fungus Collections as an international reference resource for use by scientists throughout the world. Objective 2. Develop on-line resources about the systematics of fungi, especially plant pathogens of importance to scientists and plant quarantine officials.


1b.Approach (from AD-416)
Objective 1. At the U.S. National Fungus Collections standard procedures are followed as detailed in reference books. Newly acquired specimens are “fumigated” by freezing prior to accessioning. Information about each newly acquired specimen at the U.S. National Fungus Collections (BPI) is entered in the Specimen Database with its unique accession number and barcode sticker. The dried fungal specimens are placed in acid-free boxes or in packets made of archival paper and the label is attached. Specimens are housed in standard metal herbarium cabinets on moveable compactors in limited climate-controlled space. The loan policy and guidelines of the U.S. National Fungus Collections are posted on the SMML Web site. Student technicians assist with filing specimens, pulling and mailing loans, and upgrading specimens. Newly acquired specimens and returned loans are frozen to prevent pest infestation before being incorporated into the collection. The herbarium is monitored for pests and specimens are frozen as necessary. Requests to use material for DNA analysis are considered favorably as long as sufficient material exists to support such work without jeopardizing the integrity of the specimen. Excess DNA is to be returned to the U.S. National Fungus Collections where it is stored in a –80 C freezer.

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.


3.Progress Report
Specimens in the U.S. National Fungus Collections and the on-line resources about fungi on plants serve research scientists and plant quarantine experts throughout the world. In FY08 about 65 loans were sent nationally and internationally with an equal number returned, frozen for fumigation, and re-filed. In addition, about 700 new specimens including type specimens were accessioned. About 30,000 new fungus-host reports were added to the worldwide database of fungi on plants around the world for a total of over 620,000 reports representing a comprehensive database of reports of fungi on plants. The nomenclature of about 2,700 scientific names of fungi on plants was verified allowing users to synthesize data reported for synonymous names of one species. All data is available at: http://nt.ars-grin.gov/fungaldatabases/index.cfm. Numerous questions about fungi were answered from plant and forest pathologists, mycologists, and plant quarantine officials.

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.


4.Accomplishments
1. Worldwide synopsis of Phytophthora with emphasis on species that threaten the U.S.

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
None.


6.Technology Transfer

Number of Web Sites Managed3
Number of Non-Peer Reviewed Presentations and Proceedings3
Number of Newspaper Articles and Other Presentations for Non-Science Audiences1

Review Publications
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.

Last Modified: 9/20/2014
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