Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora

Abstract

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.

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

“…Additional tools for manipulating DNA sequence data and for visualization of geographic distribution of isolates are available, as they are for the Phytophthora plant pathogen database (62). The Biolomics software package, utilized in the CBS strain database (http://www.cbs.knaw.nl/fungi/BioloMICS .aspx?searchoptϭ4), provides a wide array of additional tools, including simultaneous searches with multiple loci utilizing the "multiple sequences" tool and searches against all of the accession numbers within the entire CBS fungal culture collection.…”

A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex

“…Given the high level of phylogenetic diversity and large number of formae speciales, multilocus DNA sequence typing (MLST) currently represents the most robust approach for characterizing the genetic diversity of the FOSC. Moreover, DNA sequence data are ideally suited for sharing and developing web-accessible databases for the purpose of pathogen identification and strain typing via the Internet (Taylor and Fisher, 2003;Geiser et al, 2004;Park et al, 2008). Towards this end, the primary objective of the present study was focused on assessing the utility of partial translation elongation factor (EF-1a, 634 bp alignment) and nearly full-length nuclear ribosomal DNA intergenic spacer (IGS rDNA, 2220 bp alignment) region sequences for developing a two-locus database for the identification of formae speciales, opportunistic pathogens of humans and other animals, and environmental contaminants of hospital plumbing systems or food and beverage processing facilities.…”

The Taxonomy and Biology of Phytophthora and Pythium

“…In Phytophthora, useful websites have been developed 28,29 to allow species identification by BLAST against the collections in GenBank based primarily on similarity coefficient of the sequential analysis of the rDNA, especially the ITS region. However, the sequences housed in GenBank have not been carefully curated and mistakes could be made but this approach still seems to be the most promising as long as the isolates deposited could be checked for accuracy in identification and other molecular markers used more often by other researchers.…”

“…Attempts were made to develop a cyberinfrastructure to facilitate the identification of Phytophthora species based solely on molecular data. Thus, Park et al, 28 used the Phytophthora sequence database to develop a website: (www.phytophthoradb.org), whereas Grünwald et al, 29 introduced another website: (www.Phytophthora-ID.org). Furthermore, there was a movement to shift from the six artificial morphological groups of Waterhouse 22 to the establishment of phylogenetic clades of Phytophthora based on the molecular data to reflect a natural classification of special note is the establishment of eight clades established by Kroon et al, 30 to be followed by ten clades by Blair et al, 31 and the existence of 10 clades among Phytophthora species is now well recognized.…”