Tool background and scope

Accurate identification of species is fundamental not only for disease management, but also for the implementation of regulatory measures to prevent pathogen spread. Given the swift increase in international trade, rapid responses based on accurate pathogen identification are critical for protecting agriculture and natural ecosystems from the spread of devastating diseases. One of the most challenging aspects of working with Phytophthora species is identifying them correctly; it requires extensive training and experience. Many diagnostic laboratories, both in the U.S. and around the world, lack this type of training and frequently will only identify unknown cultures to the genus level. This could inadvertently allow species of concern to slip through undetected. Species complexes (e.g., P. boehmeriae, P. citricola, P. capsici, P.crytogea/P.dreschleri, P. megasperma, and P. parsiana) make molecular identification of species and implementation of diagnostics systems very difficult. Furthermore, many DNA sequences from incorrectly identified Phytophthora specimens are available in public databases such as NCBI. Having sequences from the type specimens is essential for accurate molecular identification of species in the genus.

IDphy was developed to facilitate accurate and efficient identification to species for the genus, using the type specimens from the original descriptions wherever possible. IDphy emphasizes species of high economic impact and species of regulatory concern for the U.S. The tool includes DNA sequence-based identification support based on ITS rDNA and COI on each of the fact sheets; an interactive Lucid key along with a tabular key; images; morphology and life cycle diagrams as well as growth, storage, and sporulation protocols; and a detailed glossary. To further support molecular identification, we have also provided SOPs and strategies to obtain a higher level of confidence in the determination of unknown species. IDphy is useful for scientists around the world, particularly those working in diagnostics and regulatory programs.

Since the official description in 1876 of Phytophthora infestans (Mont.) de Bary, the type species for the genus, there have been 182 described species as of May 2018. Three of these species have been lost (no specimens exist in any collection or laboratory around the world): P. japonica, P. inflata, and P. italica. In addition, there are eight species that are unculturable (P. cyperi, P. cyperi-bulbosi, P. eriugena, P. lepironiae, P. leersiae, P. oryzo-bladis, P. polygoni, and P. verrucosa), three hybrid species (P. × serendipita, P. × pelgrandis, and P. × stagnum), and three species are invalid (P. asparagi, P. hydropathica, and P. pseudopolonica). These species have not been included in phylogenetic studies, but we have provided available information in the fact sheets.

The first edition of IDphy provides support for molecular identification using sequencing analysis of two molecular markers that are commonly used for sequencing research and DNA bar-coding projects worldwide. Future updates of IDphy are planned that will include additional information for recently described species, additional nuclear and mitochondrial genes, and links to the Phytophthora Database, and there will be a forthcoming publication to clarify the status of species in the genus.