IDphy: An International Online Resource for Molecular and Morphological Identification of Phytophthora

Abstract

Phytophthora, with 203 species, is a genus of high importance in agriculture worldwide. Here we present the online resource "IDphy" (Link) developed to facilitate the correct identification of species of Phytophthora using the type specimens from the original descriptions wherever possible. IDphy emphasizes species of high economic impact and regulatory concern for the United States. IDphy presents an interactive Lucid key and a tabular key for 161 culturable species described as of May 2018, including 141 ex-types and 20 well-authenticated specimens. IDphy contains SOPs for morphological and molecular characterization, as well as a glossary, image gallery, and numerous links. Each of the 161 factsheets includes access to nomenclature, morphological and molecular features, including sequences of ITS rDNA, COI (barcoding genes), YPT1, β-tub, EF1α, L10, HSP90 and other genes. IDphy contains an innovative in silico BLAST and phylogenetic sequence analysis using NCBI. The IDphy Mobile App, released in August 2021 (free for Android or iOS) (Link) allows users to take the Lucid key into the laboratory. IDphy is the first online identification tool based on the ex-types implemented for plant pathogens. In this manuscript, we also include information for 21 new species and one hybrid described after the publication of IDphy, the status of the specimens of the Types and ex-types at international herbaria and culture collections, and the status of genomes at the GenBank (currently 153 genome assemblies which correspond to 42 described species including 16 ex-types). The model's effectiveness of the IDphy online resource and the content of this manuscript could inspire other researchers to develop additional identification tools for other important groups of plant pathogens.

An open-access T-BAS phylogeny for emerging Phytophthora species

“…castanetorum , thus allowing for a more detailed resolution of clade 12 ( Fig 3 ). This clade was previously referred to as 3b [ 16 , 33 ].…”

“…castanetorum , have been described. By incorporating these new sister species and using a multilocus approach, it has been confirmed that these four species comprise a new clade 12 [ 13 , 16 , 63 ]. The phylogeny presented here supports this conclusion, with P .…”

“…Unfortunately, many Phytophthora isolates in GenBank have either been misidentified or renamed as more studies are done [ 16 ]. We used ITS and CoxI datasets from the well- researched IDPhy types or extype collections where available.…”

“…Metadata for the taxa in the tree were collected using a custom Python script for web scraping with the package BeautifulSoup as well as manual data collection [ 55 ]. A portion of the metadata for some species was retrieved from IDPhy, a published, open-access Phytophthora database developed and curated by Gloria Abad and colleagues [ 16 , 33 ]. Metadata for some traits was summarized into a smaller number of categories to facilitate visualization.…”

“…Although multilocus sequencing generates robust phylogenies, the morphological and biological information of the associated species is still of high importance to researchers and is often left out of resulting phylogenies. The recent IDphy tool developed by Abad et al (2022) is an exception and includes a detailed Lucid key for species identification using morphology of over 160 species, detailed fact sheets with images and tools for running BLAST`searches at NCBI to identify species using multiple locus sequences [ 16 ]. This work also stressed the importance of well-curated type species in phylogenies.…”