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Phytophthora Database 2.0: Update and Future Direction

December 2013 , Volume 103 , Number  12
Pages  1,204 - 1,208

Bongsoo Park, Frank Martin, David M. Geiser, Hye-Seon Kim, Michele A. Mansfield, Ekaterina Nikolaeva, Sook-Young Park, Michael D. Coffey, Joseph Russo, Seong H. Kim, Yilmaz Balci, Gloria Abad, Treena Burgess, Niklaus J. Grünwald, Kyeongchae Cheong, Jaeyoung Choi, Yong-Hwan Lee, and Seogchan Kang

First, third, and eighteenth authors: Integrative Biosciences Graduate Program in Bioinformatics and Genomics, and third, fourth, fifth, sixth, seventh, and eighteenth authors: Department of Plant Pathology & Environmental Microbiology, Penn State, University Park, PA 16802; second author: USDA-ARS Crop Improvement and Protection Research Unit, Salinas, CA 93906; eighth author: Department of Plant Pathology & Microbiology, University of California, Riverside, CA 92521; ninth author: ZedX, Inc., Bellefonte, PA 16823; tenth author: Pennsylvania Department of Agriculture, Harrisburg, PA 17110; eleventh author: Department of Plant Science & Landscape Architecture, University of Maryland, College Park, MD 20742; twelfth author: USDA-APHIS-PPQ, Beltsville, MD 20705; thirteenth author: Center for Phytophthora Science and Management, Murdoch University, Australia; fourteenth author: USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR 97330; and fifteenth, sixteenth, and seventeenth authors: Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea.

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Accepted for publication 12 June 2013.

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, the sequence database has grown to cover 1 to 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: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) 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.

Additional keywords: culture collection, database, invasive pathogen, molecular diagnosis, population biology, systematics.

© 2013 The American Phytopathological Society