Comparison and Validation of Oomycetes Metabarcoding Primers
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Phytopythium: Molecular Phylogeny and Systematics
Persoonia 34, 2015: 25–39 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158515X685382 Phytopythium: molecular phylogeny and systematics A.W.A.M. de Cock1, A.M. Lodhi2, T.L. Rintoul 3, K. Bala 3, G.P. Robideau3, Z. Gloria Abad4, M.D. Coffey 5, S. Shahzad 6, C.A. Lévesque 3 Key words Abstract 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 COI clade K as described by Lévesque & de Cock (2004) belong to Phytopythium. Maximum likelihood and Bayesian LSU phylogenetic analysis of the nuclear ribosomal DNA (LSU and SSU) and mitochondrial DNA cytochrome oxidase Oomycetes subunit 1 (COI) as well as statistical analyses of pairwise distances strongly support the status of Phytopythium as Oomycota a separate phylogenetic entity. Phytopythium is morphologically intermediate between the genera Phytophthora Peronosporales and Pythium. It is unique in having papillate, internally proliferating sporangia and cylindrical or lobate antheridia. Phytopythium The formal transfer of clade K species to Phytopythium and a comparison with morphologically similar species of Pythiales the genera Pythium and Phytophthora is presented. A new species is described, Phytopythium mirpurense. SSU Article info Received: 28 January 2014; Accepted: 27 September 2014; Published: 30 October 2014. INTRODUCTION establish which species belong to clade K and to make new taxonomic combinations for these species. To achieve this The genus Pythium as defined by Pringsheim in 1858 was goal, phylogenies based on nuclear LSU rRNA (28S), SSU divided by Lévesque & de Cock (2004) into 11 clades based rRNA (18S) and mitochondrial DNA cytochrome oxidase1 (COI) on molecular systematic analyses. -
Assessment of Forest Pests and Diseases in Protected Areas of Georgia Final Report
Assessment of Forest Pests and Diseases in Protected Areas of Georgia Final report Dr. Iryna Matsiakh Tbilisi 2014 This publication has been produced with the assistance of the European Union. The content, findings, interpretations, and conclusions of this publication are the sole responsibility of the FLEG II (ENPI East) Programme Team (www.enpi-fleg.org) and can in no way be taken to reflect the views of the European Union. The views expressed do not necessarily reflect those of the Implementing Organizations. CONTENTS LIST OF TABLES AND FIGURES ............................................................................................................................. 3 ABBREVIATIONS AND ACRONYMS ...................................................................................................................... 6 EXECUTIVE SUMMARY .............................................................................................................................................. 7 Background information ...................................................................................................................................... 7 Literature review ...................................................................................................................................................... 7 Methodology ................................................................................................................................................................. 8 Results and Discussion .......................................................................................................................................... -
Tesis 1407.Pdf
Naturalis Repositorio Institucional Universidad Nacional de La Plata http://naturalis.fcnym.unlp.edu.ar Facultad de Ciencias Naturales y Museo Caracterización de especies fitopatógenas de Pythium y Phytophthora (Peronosporomycetes) en cultivos ornamentales del Cinturón verde de La Plata-Buenos Aires y otras áreas y cultivos de interés Palmucci, Hemilse Elena Doctor en Ciencias Naturales Dirección: Wolcan, Silvia Co-dirección: Steciow, Mónica Facultad de Ciencias Naturales y Museo 2015 Acceso en: http://naturalis.fcnym.unlp.edu.ar/id/20171205001560 Esta obra está bajo una Licencia Creative Commons Atribución-NoComercial-CompartirIgual 4.0 Internacional Powered by TCPDF (www.tcpdf.org) CARACTERIZACIÓN DE ESPECIES FITOPATÓGENAS DE PYTHIUM Y PHYTOPHTHORA (PERONOSPOROMYCETES) EN CULTIVOS ORNAMENTALES DEL CINTURÓN VERDE LA PLATA-BUENOS AIRES Y OTRAS ÁREAS Y CULTIVOS DE INTERÉS TESIS PARA OPTAR AL TÍTULO DE DOCTOR EN CIENCIAS NATURALES FACULTAD DE CIENCIAS NATURALES Y MUSEO UNIVERSIDAD NACIONAL DE LA PLATA HEMILSE ELENA PALMUCCI DIRECTOR: ING. AGR. SILVIA WOLCAN CODIRECTOR: DRA MÓNICA STECIOW AÑO 2015 1 AGRADECIMIENTOS A la Facultad de Ciencias Naturales y Museo (FCNYM) por brindarme la posibilidad de realizar este trabajo A la Ing Agr Silvia Wolcan y a la Dra Mónica Steciow por sus sugerencias y comentarios en la ejecución y escritura de esta tesis. A la Dra Gloria Abad, investigadora líder en Oomycetes en el “USDA- Molecular Diagnostic Laboratory (MDL)”, por su invalorable y generosa colaboración en mi formación a través de sus conocimientos, por brindarme la posibilidad de llevar a cabo los trabajos moleculares en el MDL-Maryland-USA y apoyar mi participación en workshops internacionales y reuniones de la especialidad. -
Can Phytophthora Quercina Have a Negative Impact on Mature Pedunculate Oaks Under Field Conditions? Ulrika Jönsson-Belyazio, Ulrika Rosengren
Can Phytophthora quercina have a negative impact on mature pedunculate oaks under field conditions? Ulrika Jönsson-Belyazio, Ulrika Rosengren To cite this version: Ulrika Jönsson-Belyazio, Ulrika Rosengren. Can Phytophthora quercina have a negative impact on mature pedunculate oaks under field conditions?. Annals of Forest Science, Springer Nature (since 2011)/EDP Science (until 2010), 2006, 63 (7), pp.661-672. hal-00884017 HAL Id: hal-00884017 https://hal.archives-ouvertes.fr/hal-00884017 Submitted on 1 Jan 2006 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Ann. For. Sci. 63 (2006) 661–672 661 c INRA, EDP Sciences, 2006 DOI: 10.1051/forest:2006047 Original article Can Phytophthora quercina have a negative impact on mature pedunculate oaks under field conditions? Ulrika J¨ -B*, Ulrika R Plant Ecology and Systematics, Department of Ecology, Ecology Building, Lund University, 223 62 Lund, Sweden (Received 26 September 2005; accepted 10 March 2006) Abstract – Ten oak stands in southern Sweden were investigated to evaluate the impact of the root pathogen Phytophthora quercina on mature oaks under field conditions. Phytophthora quercina was present in five of the stands, while the other five stands were used as controls to verify the effect of the pathogen. -
Alnus Glutinosa
bioRxiv preprint doi: https://doi.org/10.1101/2019.12.13.875229; this version posted December 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Investigations into the declining health of alder (Alnus glutinosa) along the river Lagan in Belfast, including the first report of Phytophthora lacustris causing disease of Alnus in Northern Ireland Richard O Hanlon (1, 2)* Julia Wilson (2), Deborah Cox (1) (1) Agri-Food and Biosciences Institute, Belfast, BT9 5PX, Northern Ireland, UK. (2) Queen’s University Belfast, Northern Ireland, UK * [email protected] Additional key words: Plant health, Forest pathology, riparian, root and collar rot. Abstract Common alder (Alnus glutinosa) is an important tree species, especially in riparian and wet habitats. Alder is very common across Ireland and Northern Ireland, and provides a wide range of ecosystem services. Surveys along the river Lagan in Belfast, Northern Ireland led to the detection of several diseased Alnus trees. As it is known that Alnus suffers from a Phytophthora induced decline, this research set out to identify the presence and scale of the risk to Alnus health from Phytophthora and other closely related oomycetes. Sampling and a combination of morphological and molecular testing of symptomatic plant material and river baits identified the presence of several Phytophthora species, including Phytophthora lacustris. A survey of the tree vegetation along an 8.5 km stretch of the river revealed that of the 166 Alnus trees counted, 28 were severely defoliated/diseased and 9 were dead. -
Presidio Phytophthora Management Recommendations
2016 Presidio Phytophthora Management Recommendations Laura Sims Presidio Phytophthora Management Recommendations (modified) Author: Laura Sims Other Contributing Authors: Christa Conforti, Tom Gordon, Nina Larssen, and Meghan Steinharter Photograph Credits: Laura Sims, Janet Klein, Richard Cobb, Everett Hansen, Thomas Jung, Thomas Cech, and Amelie Rak Editors and Additional Contributors: Christa Conforti, Alison Forrestel, Alisa Shor, Lew Stringer, Sharon Farrell, Teri Thomas, John Doyle, and Kara Mirmelstein Acknowledgements: Thanks first to Matteo Garbelotto and the University of California, Berkeley Forest Pathology and Mycology Lab for providing a ‘forest pathology home’. Many thanks to the members of the Phytophthora huddle group for useful suggestions and feedback. Many thanks to the members of the Working Group for Phytophthoras in Native Habitats for insight into the issues of Phytophthora. Many thanks to Jennifer Parke, Ted Swiecki, Kathy Kosta, Cheryl Blomquist, Susan Frankel, and M. Garbelotto for guidance. I would like to acknowledge the BMP documents on Phytophthora that proceeded this one: the Nursery Industry Best Management Practices for Phytophthora ramorum to prevent the introduction or establishment in California nursery operations, and The Safe Procurement and Production Manual. 1 Title Page: Authors and Acknowledgements Table of Contents Page Title Page 1 Table of Contents 2 Executive Summary 5 Introduction to the Phytophthora Issue 7 Phytophthora Issues Around the World 7 Phytophthora Issues in California 11 Phytophthora -
Distribution and Severity of Alder Phytophthora in Alaska1
Proceedings of the Sudden Oak Death Fourth Science Symposium Distribution and Severity of Alder 1 Phytophthora in Alaska G.C. Adams,2 M. Catal,2 and L. Trummer3 Abstract In Alaska, an unprecedented dieback and mortality of Alnus incana ssp. tenuifolia has occurred which stimulated an effort to determine causal agents of the disease. In Europe, similar dieback and mortality of Alnus incana and Alnus glutinosa has been attributed to root rot by a spectrum of newly emergent strains in the hybrid species Phytophthora alni. The variable hybrids of P. alni were grouped into three subspecies: P. alni ssp. alni (PAA), P. alni ssp. multiformis (PAM), and P. alni ssp. uniformis (PAU). From 2007 to 2008, we conducted a survey of Phytophthora species at 30 locations with stream baiting as used in the 2007 national Phytophthora ramorum Early Detection Survey for Forests in the United States. Additionally, Phytophthora species from saturated rhizosphere soil beneath alder stands were baited in situ using rhododendron leaves. We discovered PAU in rhizosphere soils in 2007 at two sample locations in unmanaged stands hundreds of miles apart, on the Kenai Peninsula and near Denali National Park. PAA was reported to be the most aggressive and pathogenic to alders and PAM and PAU were significantly less aggressive than PAA, though still pathogenic. To ascertain whether PAU was of restricted distribution due to recent introduction, or widespread distribution, we extended the survey in 2008 to 81 locations. Intensive sampling was conducted at five alder stands exhibiting dieback and 10 alder genets per location were excavated to expose nearly the entire root system for evaluation of the severity of root rot, ELISA detection of Phytophthora in diseased roots, and isolation of Phytophthora species. -
Alder Canopy Dieback and Damage in Western Oregon Riparian Ecosystems
Alder Canopy Dieback and Damage in Western Oregon Riparian Ecosystems Sims, L., Goheen, E., Kanaskie, A., & Hansen, E. (2015). Alder canopy dieback and damage in western Oregon riparian ecosystems. Northwest Science, 89(1), 34-46. doi:10.3955/046.089.0103 10.3955/046.089.0103 Northwest Scientific Association Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Laura Sims,1, 2 Department of Botany and Plant Pathology, Oregon State University, 1085 Cordley Hall, Corvallis, Oregon 97331 Ellen Goheen, USDA Forest Service, J. Herbert Stone Nursery, Central Point, Oregon 97502 Alan Kanaskie, Oregon Department of Forestry, 2600 State Street, Salem, Oregon 97310 and Everett Hansen, Department of Botany and Plant Pathology, 1085 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 Alder Canopy Dieback and Damage in Western Oregon Riparian Ecosystems Abstract We gathered baseline data to assess alder tree damage in western Oregon riparian ecosystems. We sought to determine if Phytophthora-type cankers found in Europe or the pathogen Phytophthora alni subsp. alni, which represent a major threat to alder forests in the Pacific Northwest, were present in the study area. Damage was evaluated in 88 transects; information was recorded on damage type (pathogen, insect or wound) and damage location. We evaluated 1445 red alder (Alnus rubra), 682 white alder (Alnus rhombifolia) and 181 thinleaf alder (Alnus incana spp. tenuifolia) trees. We tested the correlation between canopy dieback and canker symptoms because canopy dieback is an important symptom of Phytophthora disease of alder in Europe. We calculated the odds that alder canopy dieback was associated with Phytophthora-type cankers or other biotic cankers. -
Soil- and Waterborne Phytophthora Species Linked to Recent
REVIEW ARTICLE Soil- and waterborne Phytophthora species linked to recent outbreaks in Northern California restoration sites A review identifies several Phytophthora species found in California wildlands and discusses approaches for preventing and diagnosing the spread of these plant pathogens. by Matteo Garbelotto, Susan J. Frankel and Bruno Scanu istorically, the release of Phytophthora species Abstract in the wild has resulted in massive die-offs of Himportant native plant species, with cascading Many studies around the globe have identified plant production facilities consequences on the health and productivity of affected as major sources of plant pathogens that may be released in the wild, ecosystems (Brasier et al. 2004; Hansen 2000; Jung with significant consequences for the health and integrity of natural 2009; Lowe 2000; Rizzo and Garbelotto 2003; Swiecki ecosystems. Recently, a large number of soilborne and waterborne et al. 2003; Weste and Marks 1987). Once introduced, species belonging to the plant pathogenic genus Phytophthora have plant pathogens in general cannot be eradicated (Cun- been identified for the first time in California native plant production niffe et al. 2016; Garbelotto 2008), and costs associated facilities, including those focused on the production of plant stock used with the spread and control of exotic pathogens and in ecological restoration efforts. Additionally, the same Phytophthora pests have been estimated to surpass $100 billion per species present in production facilities have often been identified in failing year for the United States alone (Pimentel et al. 2005). restoration projects, further endangering plant species already threatened Thus, preventing the introduction of pathogens by us- or endangered. To our knowledge, the identification of Phytophthora ing pathogen-free plant stock is the most cost-effective species in restoration areas and in plant production facilities that produce and responsible approach (Parnell et al. -
Analyses of Hybrid Viability Across a Hybrid Zone Between Two Alnus Species Using Microsatellites and Cpdna Markers
G C A T T A C G G C A T genes Article Analyses of Hybrid Viability across a Hybrid Zone between Two Alnus Species Using Microsatellites and cpDNA Markers Jan Šmíd 1, Jan Douda 1, Karol Krak 1,2 and Bohumil Mandák 1,2,* 1 Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic; [email protected] (J.Š.); [email protected] (J.D.); [email protected] (K.K.) 2 Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43 Pr ˚uhonice,Czech Republic * Correspondence: [email protected] Received: 18 June 2020; Accepted: 6 July 2020; Published: 9 July 2020 Abstract: Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the variability of microsatellites and chloroplast DNA between these species and their putative hybrids to create an overall picture of the development of the hybrid zone and its predicted type. To elucidate the gene transfer within both species, the origins of individual ploidies and especially the role of triploid hybrids, a germination experiment was carried out linked with a flow cytometry study of the resulting seedlings. The tension zone model seems to offer the most adequate explanation of our observations, with selection against triploid hybrids and the spatial positioning of the hybrid zone. -
Genotypic Diversity of Common Phytophthora Species in Maryland Nurseries and Characterization of Fungicide Efficacy
ABSTRACT Title of Document: GENOTYPIC DIVERSITY OF COMMON PHYTOPHTHORA SPECIES IN MARYLAND NURSERIES AND CHARACTERIZATION OF FUNGICIDE EFFICACY Justine R. Beaulieu, Master of Science, 2015 Directed By: Assistant Professor, Dr. Yilmaz Balci, Department of Plant Science and Landscape Architecture The genetic diversity of P. plurivora, P. cinnamomi, P. pini, P. multivora, and P. citrophthora, five of the most common species found in Maryland ornamental nurseries and mid-Atlantic forests, was characterized using amplified fragment length polymorphism (AFLP). Representative isolates of genotypic clusters were then screened against five fungicides commonly used to manage Phytophthora. Three to six populations were identified for each species investigated with P. plurivora being the most diverse and P. cinnamomi the least. Clonal groups that originated from forest or different nurseries suggest an ongoing pathway of introduction. In addition, significant molecular variation existed for some species among nurseries an indication that unique genotypes being present in different nurseries. Insensitive isolates to fungicides were detected with P. plurivora (13), P. cinnamomi (3), and P. multivora (2). Interestingly, insensitive isolates primarily belonged to the least common genotypic clusters. Because all but two isolates were sensitive to dimethomorph and ametoctradin, the ability of these chemicals to manage Phytophthora is promising. Nevertheless, the presence of two insensitive isolates could portend general insensitivity to these chemicals -
Misconceptions Regading Three Levels Of
ПРИЛОЗИ, Одделение за природно-математички и биотехнички науки, МАНУ, том 40, бр. 1, стр. 93–103 (2019) CONTRIBUTIONS, Section of Natural, Mathematical and Biotechnical Sciences, MASA, Vol. 40, No. 1, pp. 93–103 (2019) Received: November 26, 2018 ISSN 1857–9027 Accepted: February 11, 2019 e-ISSN 1857–9949 UDC: 634.11-244.42(497.7)"2013/2017 634.53-244.42(497.7)"2013/2017 DOI: 10.20903/csnmbs.masa.2019.40.1.133 Original scientific paper PHYTOPHTHORA CACTORUM (LEBERT & COHN) J. SCHRÖT AS CAUSAL AGENT OF DIEBACK OF CHESTNUT AND APPLE TREES IN MACEDONIA# Mihajlo Risteski1*, Stephen Woodward2, Marin Ježić3, Rade Rusevski4, Biljana Kuzmanovska4, Kiril Sotirovski1 1Faculty of Forestry, Ss. Cyril and Methodius University, Skopje, Republic of Macedonia 2The Institute of Biological and Environmental Sciences, University of Aberdeen, Scotland 3Faculty of Science, University of Zagreb, Croatia 4Faculty of Agricultural Sciences and Food, Ss. Cyril and Methodius University, Skopje, Republic of Macedonia *e-mail: [email protected] From 2013–2017, 11 chestnut populations and 16 apple orchards/plantations in Macedonia were examined for health; soil, root and bark samples were collected from trees expressing symptoms regarded as Phytophthora specific. Using leaf baits of Prunus laurocerasus and selective V8 Agar (PARPNH), 19 pure Phytophthora sp. cultures were isolated and identified as P. cactorum by ITS sequencing. Sixteen isolates were from apple trees and 3 from chestnut trees. Phylogenetic analyses suggested slight distance between P. cactorum isolates originating from chestnut trees compared to those from apple orchards. Assessment of pathogenicity using chestnuts twigs showed no differences be- tween P. cactorum isolates from the two tree host species.