About this tool

Acknowledgments

IDphy was developed through collaboration between the USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory (PPCDL) (former Beltsville Laboratory) and the USDA APHIS PPQ S&T Identification Technology Program (ITP) at the S&T Pest Identification Technology Laboratory. Funding was provided by USDA through the Farm Bill in 2013 and 2014.

Lead author Dr. Gloria Abad would like to thank her co-authors: Dr. Treena Burgess for extraordinary support implementing the fact sheets for numerous species that she described; Dr. John Bienapfl for support developing the glossary and molecular SOPs and for generating sequences; and Ms Amanda Redford for outstanding work implementing the website and many other contributions.

Very special acknowledgements are presented by Gloria Abad to Dr. Tyler Bourret at the Department of Plant Pathology, University of California, Davis for “outstanding” work preparing the multigenic phylogenetic trees with seven genes in the factsheets of each of the 212 species that the updated IDphy V2 contains. Special acknowledgments are presented to Ms Leandra Knight for “outstanding” contributions assisting with the fact sheets, including taking photos of the cultures, adding links for voucher sequences, and content for host and distribution, and to Dr. Michael Coffey, former curator at the “World Phytophthora Collection” at University of California, Riverside for facilitating the acquisition of many cultures of the ex-holotypes and other selected specimens used for the implementation of the online resource. Both researchers were “excellent” contributors for the first phase of IDphy released in 2019.

Dr. Treena Burgess thanks past and present staff and students in the Phytophthora Science and Management, Murdoch University, Perth, Western Australia, for contributions in her research with Phytophthora.

Special acknowledgments are presented to former members of the S&T PPCDL, including Dr. Subodh Srivastava, former Bioinformatician, for his outstanding contributions submitting more than 1000 sequences of seven genes to NCBI, along with whole genome sequences (WGS) of ten ex-types in manuscripts Srivastaba et al. 2020 and Srivastava et al. 2022 and P. constricta, P. macrochlamydospora, and P. quininea (manuscript in progress); to Schyler Nunziata for “exceptional” help with the implementation of the WGS of P. castanetorum, P. quercina, P. tubulina, P. versiformis for projects lead by John Bienapfl; to M.Sc. Krysta Jennings for her “outstanding” contributions toward IDphy from February 2016 to January 2018 maintaining the culture collection on four different media, generating myceliamycelium:
mass of hyphae constituting the body, or thallus, of fungi and oomycetes; in Phytophthora species, mycelia is coenocytic
for DNA extractions, processing PCR amplifications and sequence analysis with seven genes, assisting with photography of cultures and reproductive structures, and adding data to the website in its earliest stages of development; to Dr. Reny Mathew for her “outstanding” contributions toward IDphy V2. Special acknowledgment is presented to M.Sc. Beth Kasiborski of the S&T PPCDL for her “outstanding” contributions toward IDphy V2 maintaining the culture collection of the PPCDL and submitting specimens of the ex-types to International Collections of the CBS Westerdijk Fungal Biodiversity Institute (CBS) and USDA ARS Culture Collection (NRRL), generating myceliamycelium:
mass of hyphae constituting the body, or thallus, of fungi and oomycetes; in Phytophthora species, mycelia is coenocytic
for DNA extractions, processing PCR amplifications and sequence analysis with seven genes, and assisting with photography of cultures and reproductive structures.

Additional special acknowledgements are presented to Clinton Greub (former Beltsville Laboratory scientist) for setting up the system to document the photographs of colonycolony:
assemblage of hyphae which usually develops form a single source and grows in a coordinated way
morphology for IDphy, and M.Sc. Marco Galvez (S&T PPCDL) for his special contribution processing some of the sequences submitted by the laboratory for this project.

For questions about website access or functionality, please contact ITP (itp@usda.gov).

This work would not have been possible without the help of numerous scientists, which we attempted to list on this page. The efforts of everyone listed here are greatly appreciated, and we apologize in advance if anyone who contributed to this project was omitted.

The authors express their appreciation to the following contributors who provided support for the implementation of IDphy:

Dr. Yilmaz Balci (USDA APHIS PPQ, formerly at University of Maryland) for his exceptional contributions at the early stages of the development of IDphy.
Vickie Brewster (USDA APHIS PPQ Pest, Pathogens and Biocontrol Permits) for providing support in the implementation of an early version of the Lucid key (with 128 species) based on the tabular key developed by Gloria Abad and for taking morphology photos of many species.
Dr. Jin-Hsing Huang at the Taiwan Agricultural Research Institute for refining the morphological methods designed by Gloria Abad.
Dr. Leonardo Schena at Agrarian Department, Mediterranean University Reggio Calabria, Italy for providing a new set of primers for the RAS-related protein gene (YPT1).
Dr. Scot Nelson at University of Hawaii for the contribution of numerous photos with symptoms of diseases caused by Phytophthora species.
Very special acknowledgements are presented to Drs. Konstanze Bensch (MycoBank) and Gerard Verkleij (CBS) at Westerdijk Fungal Biodiversity Institute, Netherlands for advising with items of nomenclature, typification, and collections at the CBS for all species in IDphy.
Very special acknowledgement is presented to Dr. Kirk Broders at the Agricultural Research Service, NRRL for facilitating the deposits of specimens of the ex-types into the collection and the reception of specimens from the CBS collection.
Dr. Santa Olga Cacciola, Associate Professor of Plant Pathology at the Department of Agriculture, Food, and Environment, University of Catania, Italy, for providing selected isolates of Phytophthora cambivora A1 and A2 from Italy and for providing photos of the species she recently described: P. lacustris, P. mekongensis, P. oleae, P. prodigiosa, P. tyrrhenica, and P. vulcanica.
Dr. Ronald French at USDA APHIS PPQ Plant Germplasm Quarantine Program in Beltsville, Maryland, USA for contributing numerous photos with symptoms of diseases caused by P. infestans and P. capsici.
Drs. Sara Green and April Amstrong at Centre for Forestry and Climate Change (CFCC), Forest Research, Northern Res. Station, Roslin, Scotland for providing photos of hosts infected with Phytophthora austrocedri in Scotland.
Drs. Bruno Scanu and Antonio Franceschini at Università degli Studi di Sassari, Italy for providing photos of hosts affected by Phytophthora cambivora in Italy and for photos of morphology and disease symptoms of several other Phytophthora species.
Dr. Nicholas Brazee at Center for Agriculture, Food, and the Environment, University of Massachusetts, Amherst, MA for providing photos of the morphology of asexual and sexual phases of Phytophthora caryae.
Drs. Alfredo Cravador and Dina Neves, Universidade do Algarve-FCT, Portugal for providing photos of hosts affected by Phytophthora cinnamomi in Alentejo region, Portugal.
Dr. Beatrice Henricot at The Royal Horticultural Society, Wisley, Surrey, UK for providing photos of Phytophthora pachypleura.
Dr. Lucas A. Shuttleworth at University of Sidney, Australia for providing photos of Phytophthora gondwanensis.
Drs. Koji Kageyama, Mohammad Z. Rahman, and Meherun Naher at Gifu University, Japan for providing photos of P. asiatica, P. chrysanthemi, P. lilii, P. nagai, and P. psuedolactucae.
Dr. Paul Reeser at Oregon State University for providing photos of P. borealis, P. chlamydospora, P. nemorosa, P. pluvialis, P. riparia, P. rosacearum, P. sansomeana, and P. siskiyouensis.

The following individuals provided very helpful reviews of a beta version of this website, including the associated keys and SOPs, and we thank them for their suggestions and contributions: Cheryl Blomquist, California Department of Food and Agriculture; Tyler Bourret, University of California-Davis; Tom Creswell, Purdue University; Sylvia Fernandez-Pavia, Universidad Michoacana, Mexico; Pablo Grijalba, University of Buenos Aires, Argentina; Karen Rane, University of Maryland; Hemilse Palmucci, University of Buenos Aires, Argentina; and Barbara Shew, Mike Munster, and Ella Reeves, North Carolina State University.

Special thanks to the executives of USDA APHIS PPQ: Mark Davidson, Deputy Administrator, Plant Protection and Quarantine; Wendy Jin, Associate Deputy Administrator, Science and Technology; Mark Nakhla, Director, S&T PPCDL; and Rick Zink, Director, S&T PITL, for the encouragement and support for the many years of work that have gone into the implementation of this valuable online resource.

Gloria Abad and collaborators present a very special acknowledgement to Yazmín Rivera, PPCDL Assistant Director, for the continuous support and stimulus for the major accomplishments on Phytophthora, including IDphy online resource, Plant Disease manuscript (link) and the “Revision of the Taxonomy and Phylogeny of Phytophthora” (In progress). Special acknowledgements are also presented to Vessela Mavrodieva, PPCDL Assistant Director, and Kurt Zeller, Beltsville Lab Mycology Section Supervisor, for the encouragement and stimulus for IDphy work during 2018-2019.

In progress

Dr. Abad is continuing to collect and add photographs for the fact sheets. The authors of IDphy would like to request photographic material for morphology and disease symptoms for species that are missing documentation. Proper acknowledgement will be presented in each photo and in this section. Please contact Gloria Abad if you are interested in contributing images.