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United States Department of Agriculture

Agricultural Research Service

Research Project: Detection and Management of Pathogens in Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: Phytophthora Database 2.0: update and future direction)

Author
item Park, Bongsoo
item Martin, Frank
item Geiser, David
item Kim, Hye-seon
item Mansfield, Michele
item Nikolaeva, Ekaterina
item Park, Sook-young
item Coffey, Mike
item Russo, Joseph
item Kim, Seong
item Balci, Yilmaz
item Abad, Gloria
item Burgess, Treena
item Grunwald, Niklaus - Nik
item Cheong, Kyeongchae
item Choi, Jaeyoung
item Lee, Yong-hwan
item Kang, Seogchan

Submitted to: Phytopathology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 8/1/2013
Publication Date: 12/1/2013
Publication URL: http://handle.nal.usda.gov/10113/60698
Citation: Park, B., Martin, F.N., Geiser, D., Kim, H., Mansfield, M., Nikolaeva, E., Park, S., Coffey, M., Russo, J., Kim, S., Balci, Y., Abad, G., Burgess, T., Grunwald, N.J., Cheong, K., Choi, J., Lee, Y., Kang, S. 2013. Phytophthora Database 2.0: update and future direction. Phytopathology. 103:1204-1208.

Interpretive Summary: This manuscript describes updates to a website devoted to the genus Phytophthora that improves its functionality and utility. Currently the website includes information about each species in the genus (what it looks like, plant hosts it is capable of attacking,...), DNA sequence information to facilitate identification and clarifying evolutionary relationships among species, word map to show distribution of species, and a section on molecular diagnostics.

Technical Abstract: The online community resource Phytophthora Database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, its sequence database has grown to cover 1-12 loci for ~2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: a) Geographic Information System tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, b) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, c) a comprehensive review of molecular diagnostics tools and relevant references, d) sequence alignments used to develop PCR-based diagnostics tools to support their utilization and new diagnostic tool development, and e) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD’s future direction.

Last Modified: 8/24/2016
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