DOCSLIB.ORG

Plant, Microbiology and Genetic Science and Technology Duccio

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Plant, Microbiology and Genetic Science and Technology Duccio View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Florence Research DOCTORAL THESIS IN Plant, Microbiology and Genetic Science and Technology section of " Plant Protection" (Plant Pathology), Department of Agri-food Production and Environmental Sciences, University of Florence Phytophthora in natural and anthropic environments: new molecular diagnostic tools for early detection and ecological studies Duccio Migliorini Years 2012/2015 DOTTORATO DI RICERCA IN Scienze e Tecnologie Vegetali Microbiologiche e genetiche CICLO XXVIII COORDINATORE Prof. Paolo Capretti Phytophthora in natural and anthropic environments: new molecular diagnostic tools for early detection and ecological studies Settore Scientifico Disciplinare AGR/12 Dottorando Tutore Dott. Duccio Migliorini Dott. Alberto Santini Coordinatore Prof. Paolo Capretti Anni 2012/2015 1 Declaration I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgment has been made in the text. Duccio Migliorini 29/11/2015 A copy of the thesis will be available at http://www.dispaa.unifi.it/ Dichiarazione Con la presente affermo che questa tesi è frutto del mio lavoro e che, per quanto io ne sia a conoscenza, non contiene materiale precedentemente pubblicato o scritto da un'altra persona né materiale che è stato utilizzato per l’ottenimento di qualunque altro titolo o diploma dell'Università o altro istituto di apprendimento, a eccezione del caso in cui ciò venga riconosciuto nel testo. Duccio Migliorini 29/11/2015 Una copia della tesi sarà disponibile presso DISPAA , sez. Patologia Vegetale ed Entomologia, http://www.dispaa.unifi.it/ 2 RIASSUNTO Parole chiave: qPCR; Phytophthora; invasive micro-organism; disease management; early detection, aerial spread, soilborn pathogen, Janzen-Connell negative density dependence hypothesis Scopi Scopo della tesi è stato l’analisi della patogenicità ed ecologia del genere Phytophthora attraverso differenti approcci molecolari. Metodi e Risultati L’efficacia di PCR quantitativa basata su una sonda TaqMan specifica per il genere è stata confermata come preciso strumento di rilevamento di DNA di Phytophthora su suolo artificialmente infettato, in suolo di invasatura contaminato proveniente da vivaio ed in campioni di trappole aeree. Nessuna quantificazione di DNA è avvenuta dopo due settimane dalla morte indotta del patogeno e, in confronto con i metodi di isolamento tradizionali, è stata dimostrata una significativa maggiore efficienza come strumento diagnostico. La fluttuazione stagionale di Phytophthora in aria è stata quantificata e descritta per il periodo di campionamento. La tecnica di sequenziamento 454 è stata utilizzata per identificare la tassonomia delle specie di Phytophthora in un hotspot biologico in Western Australia ed al fine di descrivere la patogenicità delle due specie sequenziate con maggior frequenza è stato realizzato un esperimento in serra. Conclusioni Le tecniche di laboratorio utilizzate in questo studio hanno fornito nuove nozioni sull’ecologia di Phytophthora. La PCR quantitativa basata su sonda TaqMan è testata e proposta come efficace strumento di prevenzione verso l’arrivo di specie invasive. Importanza dell’impatto di questo studio L’efficienza della gestione di Phytophthora dipende dalla conoscenza delle caratteristiche patogene di gruppi ristretti di specie o di una singola specie . Ricerche come queste forniscono le basi scientifiche per comprendere l’epidemiologia di una malattia ed applicare un controllo risolutivo. Lavori correlati alla Tesi. Migliorini, D., Ghelardini, L., Tondini, E., Luchi, N., & Santini, A., 2015, The potential of symptomless potted plants for carrying invasive soilborne plant pathogens, Diversity and Distributions, 21(10), 1218-1229.* * Articolo riprodotto con il permesso di Diversity and Distributions 3 ABSTRACT Key words qPCR; Phytophthora; invasive micro-organism; disease management; early detection, aerial spread, soil born pathogen, Janzen-Connell negative density dependence hypothesis Aims The purpose of my thesis was to investigate pathogenicity and ecological traits of the genus Phytophthora through molecular approaches. Methods and Results A quantitative PCR technique based on a genus specific TaqMan probe was confirmed as a precise method for detecting Phytophthora DNA in artificially infested soil under laboratory condition, in naturally infested soil and tissues of potted nursery plants and in the filters of air traps. No positive DNA quantification occurred in soil after two weeks from pathogen induced death and a significant higher efficiency as diagnostic tool was demonstrated compared to traditional isolation methods both in soil and plant tissues. Seasonal fluctuation of aerial spread of Phytophthora was also quantified and described. A 454 sequencing approach was used to identify the Phytophthora species present in a biological hotspot area in Western Australia, and a glass house experiment was performed in order to describe the pathogenicity traits of the two most frequently detected species. Conclusions The lab procedures used in this study provided a more precise knowledge of Phytophthora ecology. The quantitative PCR assay based on designed TaqMan probe was demonstrated to be very efficient and is proposed as a reliable early detection instrument of prevention against the income of invasive species. Significance of impact of the study Efficient management of Phytophthora depends to the knowledge of pathogenicity traits in restrict groups or single species. Investigations like those presented in this thesis contribute the scientific bases to understand the epidemiology of disease and to apply a successful control. Papers related to the Thesis. Migliorini, D., Ghelardini, L., Tondini, E., Luchi, N., & Santini, A., 2015, The potential of symptomless potted plants for carrying invasive soilborne plant pathogens, Diversity and Distributions, 21(10), 1218-1229.* * Article reproduced with permission of Diversity and Distributions 4 Contents Introduction................................................................................................................................................... 6 Biological cycle of Phytophthora................................................................................................................ 6 The study of Phytophthora as a plant pathogen ....................................................................................... 7 Aim............................................................................................................................................................... 10 Materials and methods................................................................................................................................ 11 I The potential of symptomless potted plants for carrying invasive soil-borne plant pathogens............ 11 II A reliable lab procedure to detect the presence of viable Phytophthora inoculum in soil samples through qPCR........................................................................................................................................... 12 III Real Time PCR detection of airborne Phytophthora species in a plant nursery area.......................... 13 IV Phytophthora distribution, taxonomy and pathogenicity within a hyperdiverse bush plant hotspot in a dune system of Western Australia........................................................................................................ 14 Results.......................................................................................................................................................... 15 I The potential of symptomless potted plants for carrying invasive soil-borne plant pathogens............ 15 II A reliable lab procedure to detect the presence of viable Phytophthora inoculum in soil samples through qPCR........................................................................................................................................... 15 III Real Time PCR detection of airborne Phytophthora species in a plant nursery area.......................... 16 IV Phytophthora distribution, taxonomy and pathogenicity within a hyperdiverse bush plant hotspot in a dune system of Western Australia........................................................................................................ 16 Discussions................................................................................................................................................... 17 Bibliography................................................................................................................................................. 18 5 Introduction Biological cycle of Phytophthora The genus Phytophthora includes fungal-like microorganisms belonging to the Oomycetes (Peronosporaceae, Peronosporales, Peronosporidae, Peronosporea, Incertae sedis, Oomycota, Chromista). These microorganisms differ from fungi in as much as they produce zygotes, from which a diploid mycelium develops, and have cell walls composed of cellulose and glucans (Agrios, 2005). Figure 1. http://forestphytophthoras.org/. Sexual reproductive long term survival spores (Oospores) are generated when the antheridium
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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 ..........................................................................................................................................
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • An Overview of Phytophthora Species Inhabiting Declining Quercus Suber Stands in Sardinia (Italy)
    Article An Overview of Phytophthora Species Inhabiting Declining Quercus suber Stands in Sardinia (Italy) Salvatore Seddaiu 1, Andrea Brandano 2, Pino Angelo Ruiu 3, Clizia Sechi 1 and Bruno Scanu 2,4,* 1 Settore Difesa Delle Piante Forestali, Agris Sardegna, Via Limbara 9, 07029 Tempio Pausania (SS), Italy; [email protected] (S.S.); [email protected] (C.S.) 2 Dipartimento di Agraria, Sezione di Patologia Vegetale ed Entomologia, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy; [email protected] 3 Settore Sughericoltura e Selvicoltura, Agris Sardegna, Via Limbara 9, 07029 Tempio Pausania (SS), Italy; [email protected] 4 Nucleo Ricerca Desertificazione, Università degli Studi di Sassari, Viale Italia 39, 07100 Sassari, Italy * Correspondence: [email protected] Received: 13 August 2020; Accepted: 4 September 2020; Published: 8 September 2020 Abstract: Cork oak forests are of immense importance in terms of economic, cultural, and ecological value in the Mediterranean regions. Since the beginning of the 20th century, these forests ecosystems have been threatened by several factors, including human intervention, climate change, wildfires, pathogens, and pests. Several studies have demonstrated the primary role of the oomycete Phytophthora cinnamomi Ronds in the widespread decline of cork oaks in Portugal, Spain, southern France, and Italy, although other congeneric species have also been occasionally associated. Between 2015 and 2019, independent surveys were undertaken to determine the diversity of Phytophthora species in declining cork oak stands in Sardinia (Italy). Rhizosphere soil samples were collected from 39 declining cork oak stands and baited in the laboratory with oak leaflets. In addition, the occurrence of Phytophthora was assayed using an in-situ baiting technique in rivers and streams located throughout ten of the surveyed oak stands.
    [Show full text]
  • Background: Threat Abatement Plan for Disease in Natural Ecosystems Caused by Phytophthora Cinnamomi
    Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi January 2014 Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi © Copyright Commonwealth of Australia, 2014 ISBN: 978-1-921733-94-9 Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi is licensed by the Commonwealth of Australia for use under a Creative Commons By Attribution 3.0 Australia licence with the exception of the Coat of Arms of the Commonwealth of Australia, the logo of the agency responsible for publishing the report, content supplied by third parties, and any images depicting people. For licence conditions see: http://creativecommons.org/licenses/by/3.0/au/. This report should be attributed as ‘Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi, Commonwealth of Australia, 2014’. The views and opinions expressed in this publication are those of the authors and do not necessarily reflect those of the Australian Government or the Minister for the Environment. The contents of this document have been compiled using a range of source materials and are valid as at August 2013. While reasonable efforts have been made to ensure that the contents of this publication are factually correct, the Commonwealth does not accept responsibility for the accuracy or completeness of the contents, and shall not be liable for any loss or damage that may be occasioned directly or indirectly through the use of, or reliance on, the contents of this publication. Photo credits Front cover: Mondurup Peak, Stirling Range, 2010 (Department of Parks and Wildlife, Western Australia) Back cover: Wildflowers on Mondurup Peak, Stirling Range, 1993 (Rob Olver) ii / Background: Threat abatement plan for disease in natural ecosystems caused by Phytophthora cinnamomi Contents 1.
    [Show full text]
  • Sequencing Abstracts Msa Annual Meeting Berkeley, California 7-11 August 2016
    M S A 2 0 1 6 SEQUENCING ABSTRACTS MSA ANNUAL MEETING BERKELEY, CALIFORNIA 7-11 AUGUST 2016 MSA Special Addresses Presidential Address Kerry O’Donnell MSA President 2015–2016 Who do you love? Karling Lecture Arturo Casadevall Johns Hopkins Bloomberg School of Public Health Thoughts on virulence, melanin and the rise of mammals Workshops Nomenclature UNITE Student Workshop on Professional Development Abstracts for Symposia, Contributed formats for downloading and using locally or in a Talks, and Poster Sessions arranged by range of applications (e.g. QIIME, Mothur, SCATA). 4. Analysis tools - UNITE provides variety of analysis last name of primary author. Presenting tools including, for example, massBLASTer for author in *bold. blasting hundreds of sequences in one batch, ITSx for detecting and extracting ITS1 and ITS2 regions of ITS 1. UNITE - Unified system for the DNA based sequences from environmental communities, or fungal species linked to the classification ATOSH for assigning your unknown sequences to *Abarenkov, Kessy (1), Kõljalg, Urmas (1,2), SHs. 5. Custom search functions and unique views to Nilsson, R. Henrik (3), Taylor, Andy F. S. (4), fungal barcode sequences - these include extended Larsson, Karl-Hnerik (5), UNITE Community (6) search filters (e.g. source, locality, habitat, traits) for 1.Natural History Museum, University of Tartu, sequences and SHs, interactive maps and graphs, and Vanemuise 46, Tartu 51014; 2.Institute of Ecology views to the largest unidentified sequence clusters and Earth Sciences, University of Tartu, Lai 40, Tartu formed by sequences from multiple independent 51005, Estonia; 3.Department of Biological and ecological studies, and for which no metadata Environmental Sciences, University of Gothenburg, currently exists.
    [Show full text]
  • Aquatic Assemblages from Edna Metabarcoding 1 Casting a Broader
    1 Running Head: Aquatic assemblages from eDNA metabarcoding 2 Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from 3 diverse taxonomic targets 4 Laura L. Hauck1†, Kevin A. Weitemier2†, Brooke E. Penaluna1, Tiffany Garcia2, and Richard Cronn1* 5 1U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, 6 Corvallis, OR 97331, email: [email protected] 7 2Oregon State University, Department of Fisheries and Wildlife, 104 Nash Hall, Corvallis, OR 97331 8 Tel: 1 (541) 737-7291 Fax: 1 (541) 750-7329 *Author for correspondence 9 †L. Hauck and K. Weitemier should be considered joint first author. 10 11 Abstract 12 Environmental DNA (eDNA) assays for single- and multi-species detection show promise for providing 13 standardized assessment methods for diverse taxa, but techniques for evaluating multiple taxonomically- 14 divergent assemblages are in their infancy. We evaluated whether microfluidic multiplex metabarcoding and 15 high-throughput sequencing could identify diverse aquatic and riparian assemblages from 48 taxon-general and 16 taxon-specific metabarcode primers. eDNA screening was paired with electrofishing along a stream continuum 17 to evaluate congruence between methods. A fish hatchery located midway along the stream continuum 18 provided a dispersal barrier, and a point source for non-native White Sturgeon (Acipencer transmontanus). 19 Microfluidic metabarcoding detected all 13 species observed by electrofishing, with overall accuracy of 86%. 20 Taxon-specific barcoding primers were more successful than taxon-general universal metabarcoding primers at 21 classifying sequences to species. Both types of markers detected a transition from downstream sites dominated 22 by multiple fish species, to upstream sites dominated by a single species; however, we failed to detect a 23 transition in amphibian population structure.
    [Show full text]
  • Norrie's Plant Descriptions - Index of Common Names a Key to Finding Plants by Their Common Names (Note: Not All Plants in This Document Have Common Names Listed)
    UC Santa Cruz Arboretum & Botanic Garden Plant Descriptions A little help in finding what you’re looking for - basic information on some of the plants offered for sale in our nursery This guide contains descriptions of some of plants that have been offered for sale at the UC Santa Cruz Arboretum & Botanic Garden. This is an evolving document and may contain errors or omissions. New plants are added to inventory frequently. Many of those are not (yet) included in this collection. Please contact the Arboretum office with any questions or suggestions: [email protected] Contents copyright © 2019, 2020 UC Santa Cruz Arboretum & Botanic Gardens printed 27 February 2020 Norrie's Plant Descriptions - Index of common names A key to finding plants by their common names (Note: not all plants in this document have common names listed) Angel’s Trumpet Brown Boronia Brugmansia sp. Boronia megastigma Aster Boronia megastigma - Dark Maroon Flower Symphyotrichum chilense 'Purple Haze' Bull Banksia Australian Fuchsia Banksia grandis Correa reflexa Banksia grandis - compact coastal form Ball, everlasting, sago flower Bush Anemone Ozothamnus diosmifolius Carpenteria californica Ozothamnus diosmifolius - white flowers Carpenteria californica 'Elizabeth' Barrier Range Wattle California aster Acacia beckleri Corethrogyne filaginifolia - prostrate Bat Faced Cuphea California Fuchsia Cuphea llavea Epilobium 'Hummingbird Suite' Beach Strawberry Epilobium canum 'Silver Select' Fragaria chiloensis 'Aulon' California Pipe Vine Beard Tongue Aristolochia californica Penstemon 'Hidalgo' Cat Thyme Bird’s Nest Banksia Teucrium marum Banksia baxteri Catchfly Black Coral Pea Silene laciniata Kennedia nigricans Catmint Black Sage Nepeta × faassenii 'Blue Wonder' Salvia mellifera 'Terra Seca' Nepeta × faassenii 'Six Hills Giant' Black Sage Chilean Guava Salvia mellifera Ugni molinae Salvia mellifera 'Steve's' Chinquapin Blue Fanflower Chrysolepis chrysophylla var.
    [Show full text]