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

Phytophthora, with 203 species, is a genus of high importance in agriculture worldwide. Here, we present the online resource "IDphy", 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 standard operating procedures for morphological and molecular characterization, as well as a glossary, image gallery, and numerous links. Each of the 161 factsheets includes access to nomenclature and morphological and molecular features, including sequences of the internal transcribed spacer ribosomal DNA, cytochrome C oxidase subunit I (barcoding genes), YPT1, ß-tubulin, elongation factor 1a, L10, heat shock protein 90, 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), 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 article, 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 effectiveness of the IDphy online resource and the content of this article could inspire other researchers to develop additional identification tools for other important groups of plant pathogens.

Genome Resources for the Ex-Type of Phytophthora citricola, and Well-Authenticated Isolates of P. hibernalis, P. nicotianae, and P. syringae.

Phytophthora is one of the most important genera of plant pathogens, with many members causing high economic losses worldwide. To build robust molecular identification systems, it is very important to have information from well-authenticated specimens and, in preference, the ex-type specimens. The reference genomes of well-authenticated specimens form a critical foundation for genetics, biological research, and diagnostic applications. In this study, we describe four draft Phytophthora genome resources for the ex-type of Phytophthora citricola BL34 (P0716 WPC) (118 contigs for 50 Mb), and well-authenticated specimens of P. syringae BL57G (P10330 WPC) (591 contigs for 75 Mb), P. hibernalis BL41G (P3822 WPC) (404 contigs for 84 Mb), and P. nicotianae BL162 (P6303 WPC) (3,984 contigs for 108 Mb) generated with MinION long-read high-throughput sequencing technology (Oxford Nanopore Technologies). Using the quality reads, we assembled high-coverage genomes of P. citricola with 291× coverage and 16,662 annotated genes; P. nicotianae with 205× coverage and 29,271 annotated genes; P. syringae with 76× coverage and 23,331 annotated genes, and P. hibernalis with 42× coverage and 21,762 annotated genes. With the availability of genome sequences and their annotations, we predict that these draft genomes will be accommodating for various basic and applied research, including diagnostics to protect global agriculture.

Draft Genome Resource for the Ex-types of Phytophthora ramorum, P. kernoviae, and P. melonis, Species of Regulatory Concern, Using Ultra-Long Read MinION Nanopore Sequencing.

Phytophthora ramorum, P. kernoviae, and P. melonis are each species of current regulatory concern in the United States, the United Kingdom, and other areas of the world. Ex-type material are cultures and duplicates of the type that was used to describe each species and that are deposited in additional culture collections. Using these type specimens as references is essential to designing correct molecular identification and diagnostic systems. Here, we report a whole genome sequence for the Ex-type material of P. ramorum, P. kernoviae, and P. melonis generated using high-throughput sequencing via the MinION third generation platform from Oxford Nanopore Technology. We assembled the quality filtered reads into contigs for each species. We assembled the continuous contigs of P. ramorum, P. kernoviae, and P. melonis (1,322, 545, and 2,091 contigs, respectively). The ab initio prediction of genes from these species reveals that there are 16,838, 12,793, and 34,580 genes in P. ramorum, P. kernoviae, and P. melonis, respectively. Of the 34,580 P. melonis genes, 10,164 genes were conserved among all three of these Phytophthora species which may include pathogenicity genes. We compared the ex-type of P. ramorum EU1 lineage assembly with another selected isolate of EU1 available at the National Center for Biotechnology Information and found 251,859 single nucleotide polymorphisms (SNPs) genome-wide; the comparison with the EU2 lineage genome isolate revealed 441,859 SNPs genome-wide. This genome resource of the ex-types of P. ramorum, and P. kernoviae is a significant contribution as these species are among the most important pathogens of regulatory concern in different regions of the world.

Draft Genome Resources for the Phytopathogenic Fungi Monilinia fructicola, M. fructigena, M. polystroma, and M. laxa, the Causal Agents of Brown Rot.

Fungi in the genus Monilinia cause brown rot disease of stone and pome fruits. Here, we report the draft genome assemblies of four important phytopathogenic species: M. fructicola, M. fructigena, M. polystroma, and M. laxa. The draft genome assemblies were 39 Mb (M. fructigena), 42 Mb (M. laxa), 43 Mb (M. fructicola), and 45 Mb (M. polystroma) with as few as 550 contigs (M. laxa). These are the first draft genome resources publicly available for M. laxa, M. fructigena, and M. polystroma.

Phytopythium: molecular phylogeny and systematics.

The genus Phytopythium (Peronosporales) has been described, but a complete circumscription has not yet been presented. In the present paper we provide molecular-based evidence that members of Pythium clade K as described by Lévesque & de Cock (2004) belong to Phytopythium. Maximum likelihood and Bayesian phylogenetic analysis of the nuclear ribosomal DNA (LSU and SSU) and mitochondrial DNA cytochrome oxidase subunit 1 (COI) as well as statistical analyses of pairwise distances strongly support the status of Phytopythium as a separate phylogenetic entity. Phytopythium is morphologically intermediate between the genera Phytophthora and Pythium. It is unique in having papillate, internally proliferating sporangia and cylindrical or lobate antheridia. The formal transfer of clade K species to Phytopythium and a comparison with morphologically similar species of the genera Pythium and Phytophthora is presented. A new species is described, Phytopythium mirpurense.

Phytophthora niederhauserii sp. nov., a polyphagous species associated with ornamentals, fruit trees and native plants in 13 countries.

A non-papillate, heterothallic Phytophthora species first isolated in 2001 and subsequently from symptomatic roots, crowns and stems of 33 plant species in 25 unrelated botanical families from 13 countries is formally described here as a new species. Symptoms on various hosts included crown and stem rot, chlorosis, wilting, leaf blight, cankers and gumming. This species was isolated from Australia, Hungary, Israel, Italy, Japan, the Netherlands, Norway, South Africa, Spain, Taiwan, Turkey, the United Kingdom and United States in association with shrubs and herbaceous ornamentals grown mainly in greenhouses. The most prevalent hosts are English ivy (Hedera helix) and Cistus (Cistus salvifolius). The association of the species with acorn banksia (Banksia prionotes) plants in natural ecosystems in Australia, in affected vineyards (Vitis vinifera) in South Africa and almond (Prunus dulcis) trees in Spain and Turkey in addition to infection of shrubs and herbaceous ornamentals in a broad range of unrelated families are a sign of a wide ecological adaptation of the species and its potential threat to agricultural and natural ecosystems. The morphology of the persistent non-papillate ellipsoid sporangia, unique toruloid lobate hyphal swellings and amphigynous antheridia does not match any of the described species. Phylogenetic analysis based on sequences of the ITS rDNA, EF-1α, and ß-tub supported that this organism is a hitherto unknown species. It is closely related to species in ITS clade 7b with the most closely related species being P. sojae. The name Phytophthora niederhauserii has been used in previous studies without the formal description of the holotype. This name is validated in this manuscript with the formal description of Phytophthora niederhauserii Z.G. Abad et J.A. Abad, sp. nov. The name is coined to honor Dr John S. Niederhauser, a notable plant pathologist and the 1990 World Food Prize laureate.

Identification and Detection of Phytophthora: Reviewing Our Progress, Identifying Our Needs.

With the increased attention given to the genus Phytophthora in the last decade in response to the ecological and economic impact of several invasive species (such as P. ramorum, P. kernoviae, and P. alni), there has been a significant increase in the number of described species. In part, this is due to the extensive surveys in historically underexplored ecosystems (e.g., forest and stream ecosystems) undertaken to determine the spread of invasive species and the involvement of Phytophthora species in forest decline worldwide (e.g., oak decline). The past decade has seen an approximate doubling in the number of described species within the genus Phytophthora, and the number will likely continue to increase as more surveys are completed and greater attention is devoted to clarifying phylogenetic relationships and delineating boundaries in species complexes. The development of molecular resources, the availability of credible sequence databases to simplify identification of new species, and the sequencing of several genomes have provided a solid framework to gain a better understanding of the biology, diversity, and taxonomic relationships within the genus. This information is much needed considering the impact invasive or exotic Phytophthora species have had on natural ecosystems and the regulatory issues associated with their management. While this work is improving our ability to identify species based on phylogenetic grouping, it has also revealed that the genus has a much greater diversity than previously appreciated.

Morphological and molecular characterization of Phytophthora glovera sp. nov. from tobacco in Brazil.

A root rot disease of cultivated tobacco called yellow stunt has been observed in the burley tobacco production areas of Brazil since the early 1990s. Root infecting fungi and straminipiles were isolated from the roots of diseased tobacco plants, including a semi-papillate, homothallic, slow growing Phytophthora species. Pathogenicity trials confirmed that Phytophthora sp. caused root rot and stunting of burley and flue-cured tobaccos. Morphological characteristics of the asexual and sexual stages of this organism did not match any reported Phytophthora species and were very different from the widely known tobacco black shank pathogen P. nicotianae. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA, ß-tubulin and translation elongation factor 1-α regions indicated that this organism represents a previously unreported Phytophthora species that is significantly supported in clade 2 and most closely related to P. capsici. However P. glovera differs from P. capsici in a number of morphological characters, most significantly P. glovera is homothallic and produces both paragynous and amphigynous antheridia while P. capsici is heterothallic and produces only amphigynous antheridia. In this paper we confirmed pathogenicity of this species on tobacco and describe the morphological and molecular characteristics of Phytophthora glovera sp. nov.

Phytophthora morindae, a new species causing black flag disease on noni (Morinda citrifolia L) in Hawaii.

A homothallic, papillate Phytophthora species causing foliar and fruit blight of noni (Morinda citrifolia var. citrifolia) in Hawaii was identified. The asexual phase of this species is characterized by the production of umbellate sporangiophores and papillate sporangia that are ellipsoid and obpyriform with conspicuously tapered bases and possess caducous, medium to long pedicels. The sexual phase is characterized by the production of oogonia with tapered bases, small amphigynous antheridia and thick-walled, plerotic oospores. The morphology of the taxon does not match any of the valid 95 Phytophthora species described to date. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA region (ITS) and the translation elongation factor 1 alpha (EF-1 alpha) of this taxon and those from other Phytophthora species from GenBank and the Phytophthora database indicates that the new taxon is most closely related to species in ITS clade 10, including P. kernoviae, P. boehmeriae and the recently described P. gallica. The most closely related species is P. kernoviae, an invasive plant pathogen causing bleeding stem lesions on forest trees (beech, Fagus sylvatica) and foliar necrosis of ornamentals (rhododendron, pieris and magnolia) in the UK, and isolated in New Zealand from necrotic cherimoya shoots and fruits and soil. Although the morphological characters of the sexual phase of P. morindae and P. kernoviae are similar, the umbellate sporangiophores produced by the new taxon marks the main morphological distinction. In this paper we describe the morphological characteristics, the phylogenetic relationships and pathogenicity characteristics that support the description of this taxon as a new species with the proposed name Phytophthora morindae sp. nov.

Phytophthora bisheria sp. nov., a new species identified in isolates from the Rosaceous raspberry, rose and strawberry in three continents.

A homothallic semipapillate slow growing Phytophthora species associated with root rot of strawberries from greenhouse-grown plants in North Carolina, USA, root rot of roses in the Netherlands, and root rot of raspberry in Knoxfield, Australia, was identified. The main character of this organism is the production of paragynous antheridia with broad attachment to the oogonial wall. The morphology of the pathogen does not match that of any of the more than 85 described Phytophthora species. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA region (ITS1-5.8S-ITS2) of this taxon and those from other Phytophthora species from GenBank supports the conclusion that this organism is an unreported new species. In the phylogenetic tree with other reported Phytophthora species at the GenBank, the new species is more closely related to others in ITS clade 2 comprising semipapillate taxa including P. botryosa, P. citrophthora, P. colocasiae, P. meadii, P. citricola, P. inflata, P.tropicalis, P. capsici, Phytophthora sp. 'glovera' and P. multivesiculata. The most closely related species is P. multivesiculata isolated from Cymbidium orchid in the Netherlands. In this paper we describe the morphological characteristics and the phylogenetic relationships that support the description of this taxon as a new species Phytophthora bisheria sp. nov.