Phytophthora: taxonomic and phylogenetic revision of the genus

Authors: ABAD, GLORIA - Animal And Plant Health Inspection Service (APHIS); BURGESS, TREENA - David H Murdock Research Institute; BOURRET, TYLERS - University Of California, Davis; BENSCH, KONSTANZE - Fungal Biodiversity; CACCIOLA, SANTA - University Of Catania; SCANU, BRUNO - University Of Sassari; MATHEW, RENY - Animal And Plant Health Inspection Services (APHIS), National Wildlife Center; KASIBORSKI, BETH - Animal And Plant Health Inspection Services (APHIS), National Wildlife Center; SRIVASTAVA, SUBODH - Animal And Plant Health Inspection Services (APHIS), National Wildlife Center; KAGEYAMA, KOJI - Gifu University; BIENAPFL, JOHN - Animal And Plant Health Inspection Services (APHIS), National Wildlife Center; VERKLEIJ, GERARD - Fungal Biodiversity; Broders, Kirk; SCHENA, LEONARDO - University Of Reggio Calabria; REDFORD, AMANDA - Animal And Plant Health Inspection Services (APHIS), National Wildlife Center

Submitted to: Studies in Mycology
Publication Type: Monograph
Publication Acceptance Date: 8/19/2023
Publication Date: 10/6/2023
Citation: Abad, Z.G., Burgess, T.I., Bourret, T., Bensch, K., Cacciola, S.O., Scanu, B., Mathew, R., Kasiborski, B., Srivastava, S., Kageyama, K., Bienapfl, J.C., Verkleij, G., Broders, K., Schena, L., Redford, A.J. 2023. Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology. 106:259–348. https://doi.org/10.3114/sim.2023.106.05.
DOI: https://doi.org/10.3114/sim.2023.106.05

Interpretive Summary: The Oomycetes are a group of fungus-like organisms that include many economically and ecologically important plant pathogens. Specifically, members of the genus Phytophthora are known to be some of the most damaging pathogens of agriculture crops, horticultural plants, and native forest species and represent a significant biosecurity concern as many species are not native to North America. In the last 30 years the number of species of Phytophthora have grown from 40 to over 200, with many new species described each year. As many of these species represent a biosecurity risk to the U.S. it is important to have a current listing of Phytophthora species with corresponding DNA sequence data to allow for rapid identification of potential new invasions. An ARS Scientist in Peoria, IL collaborated with scientists at USDA-APHIS and Universities around the world to develop a taxonomic and phylogenetic revision of the genus Phytophthora with a molecular toolbox for species identification. The researchers worked with global network of culture collections and researchers to assemble a monograph of 212 Phytophthora species with corresponding morphological, geographic and molecular data. This data was also used to update the IDPhy online resources for Phytophthora species identification and information, which makes all of this data available to scientists as well as the general public. These resources will be of interest to plant disease diagnosticians, plant pathologists, crop breeders and quarantine officials around the world as it represents a single location where all information of Phytophthora species identification can easily be accessed.

Technical Abstract: Many members of the Oomycete genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for twenty species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. xmultiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated Multigene Phylogeny and Molecular Toolbox with seven genes (ITS rDNA, ß-tub, COI, EF1a, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, culturable species (including nine hybrid taxa). The information on genomes of 23 types published at the present time is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 culturable species, are associated with the “IDphy: molecular and morphological identification of Phytophthora based on the types” online resource (Link). The first version of IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic Molecular Toolbox with 7 genes that includes the two Barcoding/Metabarcoding genes (ITS and COI) that are important for SANGER sequencing are also very valuable for High Throughput Sequencing Technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens.