@article{abad_burgess_bourret_bensch_cacciola_scanu_mathew_kasiborski_srivastava_kageyama_et al._2023, title={<i>Phytophthora</i>: taxonomic and phylogenetic revision of the genus}, volume={106}, ISSN={["1872-9797"]}, DOI={10.3114/sim.2023.106.05}, abstractNote={Many members of the Oomycota 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 20 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. ×multiformis 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, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date 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 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the 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 seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) 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. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.}, journal={STUDIES IN MYCOLOGY}, author={Abad, Z. G. and Burgess, T. I. and Bourret, T. and Bensch, K. and Cacciola, S. O. and Scanu, B. and Mathew, R. and Kasiborski, B. and Srivastava, S. and Kageyama, K. and et al.}, year={2023}, month={Dec}, pages={259–348} }
 @article{abad_burgess_redford_bienapfl_srivastava_mathew_jennings_2022, title={IDphy: An International Online Resource for Molecular and Morphological Identification of Phytophthora}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-02-22-0448-FE}, abstractNote={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.}, journal={PLANT DISEASE}, author={Abad, Z. Gloria and Burgess, Treena I. and Redford, Amanda J. and Bienapfl, John C. and Srivastava, Subodh and Mathew, Reny and Jennings, Krysta}, year={2022}, month={Jul} }
 @article{ochola_cortada_mwaura_tariku_christensen_ng'ang'a_hassanali_pirzada_khan_pal_et al._2022, title={Wrap-and-plant technology to manage sustainably potato cyst nematodes in East Africa}, volume={2}, ISSN={["2398-9629"]}, url={https://doi.org/10.1038/s41893-022-00852-5}, DOI={10.1038/s41893-022-00852-5}, abstractNote={Abstract Renewable eco-friendly options for crop protection are fundamental in achieving sustainable agriculture. Here, we demonstrate the use of a biodegradable lignocellulosic banana-paper matrix as a seed wrap for the protection of potato plants against potato cyst nematode (PCN), Globodera rostochiensis . Potato cyst nematodes are devastating quarantine pests of potato globally. In East Africa, G. rostochiensis has recently emerged as a serious threat to potato production. Wrapping seed potatoes within the lignocellulose banana-paper matrix substantially reduced G. rostochiensis field inoculum and increased potato yields by up to fivefold in Kenya, relative to farmer practice, whether or not impregnated with ultra-low doses of the nematicide abamectin (ABM). Markedly, ABM-treated banana paper at ~1,000 times lower than conventional recommendations reduced PCN inoculum. Assays and analyses revealed that the lignocellulose matrix disrupts parasite–host chemical signalling by adsorbing critical PCN hatching and infective juvenile host location chemicals present in potato root exudate. Recovery experiments confirmed adsorption of these host location chemicals. Our study demonstrates the use of waste organic material to sustainably manage PCN, and potentially other crop root pests, while increasing potato yields.}, journal={NATURE SUSTAINABILITY}, author={Ochola, Juliet and Cortada, Laura and Mwaura, Onesmus and Tariku, Meklit and Christensen, Shawn A. and Ng'ang'a, Margaret and Hassanali, Ahmed and Pirzada, Tahira and Khan, Saad and Pal, Lokendra and et al.}, year={2022}, month={Feb} }
 @article{pirzada_sohail_tripathi_farias_mathew_li_opperman_khan_2021, title={Toward Sustainable Crop Protection: Aqueous Dispersions of Biodegradable Particles with Tunable Release and Rainfastness}, volume={11}, ISSN={["1616-3028"]}, url={https://doi.org/10.1002/adfm.202108046}, DOI={10.1002/adfm.202108046}, abstractNote={Fabrication of aqueous particulate dispersions of biodegradable cellulose esters (CEs) as efficient carriers of agrochemical active‐ingredients (AIs) for foliar applications, is reported. The use of different ester substituent groups on CE permits modulation of particle morphology and size, from irregular shapes (<350 nm) to spheres (≈1.1 µm diameter), while maintaining stability as supported by minimal change in zeta potential and particle size over one year. Rainfastness is tested by simulating >50 mm h−1 rainfall on coated banana and tomato leaves and silicon. Surface coverage loss as low as 9%, based on the nature of leaf and formulation, confirms the rainfastness of the formulations. Variation in the release kinetics of a model AI fluopyram from different CEs can be attributed to the particle morphology and the nature of binding between fluopyram and various CEs. Thermodynamic analysis demonstrates spontaneous binding between fluopyram and multiple sites of CEs, justifying its two‐step release from CE particles. System functionalities are corroborated via in‐vitro fungal inhibition assays demonstrating a 100% inhibition of the fungal growth. This “lab‐to‐leaf” approach of materials development involving fundamental insights and functional performance reveals CE dispersions are promising green agricultural formulations with the potential to impact a myriad of crops around the globe.}, journal={ADVANCED FUNCTIONAL MATERIALS}, publisher={Wiley}, author={Pirzada, Tahira and Sohail, Mariam and Tripathi, Anurodh and Farias, Barbara V and Mathew, Reny and Li, Chunying and Opperman, Charles H. and Khan, Saad A.}, year={2021}, month={Nov} }
 @misc{mathew_opperman_2020, title={Current Insights into Migratory Endoparasitism: Deciphering the Biology, Parasitism Mechanisms, and Management Strategies of Key Migratory Endoparasitic Phytonematodes}, volume={9}, ISSN={["2223-7747"]}, DOI={10.3390/plants9060671}, abstractNote={Despite their physiological differences, sedentary and migratory plant-parasitic nematodes (PPNs) share several commonalities. Functional characterization studies of key effectors and their targets identified in sedentary phytonematodes are broadly applied to migratory PPNs, generalizing parasitism mechanisms existing in distinct lifestyles. Despite their economic significance, host–pathogen interaction studies of migratory endoparasitic nematodes are limited; they have received little attention when compared to their sedentary counterparts. Because several migratory PPNs form disease complexes with other plant-pathogens, it is important to understand multiple factors regulating their feeding behavior and lifecycle. Here, we provide current insights into the biology, parasitism mechanism, and management strategies of the four-key migratory endoparasitic PPN genera, namely Pratylenchus, Radopholus, Ditylenchus, and Bursaphelenchus. Although this review focuses on these four genera, many facets of feeding mechanisms and management are common across all migratory PPNs and hence can be applied across a broad genera of migratory phytonematodes.}, number={6}, journal={PLANTS-BASEL}, author={Mathew, Reny and Opperman, Charles H.}, year={2020}, month={Jun} }
 @article{mathew_opperman_2019, title={The genome of the migratory nematode, Radopholus similis, reveals signatures of close association to the sedentary cyst nematodes}, volume={14}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0224391}, abstractNote={Radopholus similis, commonly known as the burrowing nematode, is an important pest of myriad crops and ornamentals including banana (Musa spp.) and Citrus spp. In order to characterize the potential role of putative effectors encoded by R. similis genes we compared predicted proteins from a draft R. similis genome with other plant-parasitic nematodes in order to define the suite of excreted/secreted proteins that enable it to function as a parasite and to ascertain the phylogenetic position of R. similis in the Tylenchida order. Identification and analysis of candidate genes encoding for key plant cell-wall degrading enzymes including GH5 cellulases, PL3 pectate lyases and GH28 polygalactouranase revealed a pattern of occurrence similar to other PPNs, although with closest phylogenetic associations to the sedentary cyst nematodes. We also observed the absence of a suite of effectors essential for feeding site formation in the cyst nematodes. Clustering of various orthologous genes shared by R. similis with other nematodes showed higher overlap with the cyst nematodes than with the root-knot or other migratory endoparasitic nematodes. The data presented here support the hypothesis that R. similis is evolutionarily closer to the cyst nematodes, however, differences in the effector repertoire delineate ancient divergence of parasitism, probably as a consequence of niche specialization. These similarities and differences further underscore distinct evolutionary relationships during the evolution of parasitism in this group of nematodes.}, number={10}, journal={PLOS ONE}, author={Mathew, Reny and Opperman, Charles H.}, year={2019}, month={Oct} }