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Phytophthora database: a forensic database supporting the identification and monitoring of Phytophthora

TitlePhytophthora database: a forensic database supporting the identification and monitoring of Phytophthora
Publication TypeJournal Article
2008
AuthorsPark, J, Park, B, Veeraraghavan, N, Jung, K, Lee, YH, Blair, JE, Geiser, DM, Isard, S, Mansfield, MA, Nikolaeva, E, Park, SY, Russo, J, Kim, SH, Greene, M, Ivors, KL, Balci, Y, Peiman, M, Erwin, DC, Coffey, MD, Rossman, A, Farr, D, Cline, E, Grünwald, NJ, Luster, DG, Schrandt, J, Martin, F, Ribeiro, OK, Makalowska, I, Kang, S
JournalPlant Disease
Volume92
Pagination966-972
Date PublishedJun
0191-2917
ISI:000256007700017
california, culture collection, disease management, forest trees, genome sequences, invasive pathogens, leaf-blight, molecular diagnosis, pathogen, ramorum, rot, sequence alignment, sp-nov., species causing root

Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.

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