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16th Meeting of the
International Council for the Study of Virus and Virus-like
Diseases of the Grapevine
(ICVG XVI)

31 August - 4 September 2009
Dijon, France

Extended Abstracts

Le Progrès Agricole et Viticole - ISSN 0369-8173

Modifications in the layout of abstracts received from authors have been made to fit with

the publication format of Le Progrès Agricole et Viticole.

We apologize for errors that could have arisen during the editing process despite our careful vigilance.

Acknowledgements
Cover page : Olivier Jacquet Photos : Gérard Simonin
Jean Le Maguet

  • ICVG Steering Committee
  • ICVG XVI Organising committee

Giovanni, P. MARTELLI, chairman (I)
Paul GUGERLI, secretary (CH)
Giuseppe BELLI (I)
Elisabeth BOUDON-PADIEU (INRA) Silvio GIANINAZZI (INRA - CNRS)

Jocelyne PÉRARD (Chaire UNESCO Culture et
Traditions du Vin, Univ Bourgogne)

Johan T. BURGER (RSA) Marc FUCHS (F – USA) Deborah A. GOLINO (USA) Raymond JOHNSON (CA) Michael MAIXNER (D) Gustavo NOLASCO (P) Ali REZAIAN (USA) Iannis C. RUMBOS (G)
Oscar A. De SEQUEIRA (P)
Edna TANNE (IL)

Olivier JACQUET (Chaire UNESCO Culture et
Traditions du Vin, Univ Bourgogne)

Pascale SEDDAS (INRA)

Sandrine ROUSSEAUX (Institut Jules Guyot, Univ
Bourgogne)

Denis CLAIR (INRA)
Dominique MILLOT (INRA)

Xavier DAIRE (INRA – CRECEP)

Mary Jo FARMER (INRA)
Caroline CHATILLON (SEDIAG) Etienne HERRBACH (INRA Colmar) Jean Le MAGUET (INRA Colmar)
René BOVEY, Honorary secretary

Honorary committee members

Session convenors

A. CAUDWELL (F)
D. GONSALVES (USA) H.-H. KASSEMEYER (D)
G. KRIEL (RSA)
Michael MAIXNER Olivier LEMAIRE Etienne HERRBACH
Élisabeth BOUDON-PADIEU
Sandrine ROUSSEAUX
Pascale SEDDAS
D. STELLMACH, (D)
A. TELIZ, (Mex) A. VUITTENEZ (F) B. WALTER (F).

Invited speakers to ICVG XVI

Giovanni P. MARTELLI
Paul GUGERLI
Valerian V. DOLJA
Sead SABANADZOVIC Gérard DEMANGEAT
Xavier FOISSAC
Ilan SELA
Cristina CABALEIRO Pasquale SALDARELLI

Conference secretariat

Sophie NOLLOT - Sandrine GIORDANA
Alice MORISOT - Isabelle CARRÉ
INRA – UMR PME - BP 86510 – 21650 DIJON Cedex

Phone : 33 (0)380 69 34 40 / 33 (0)380 69 30 00
Fax: 33-(0)380 69 37 53

E-mail : [email protected] https://colloque2.inra.fr/icvg16

ICVG website : http://www.icvg.ch

AVANT-PROPOS

Nous sommes très heureux que le choix du Comité de direction de l'ICVG se soit porté sur Dijon pour la tenue de sa 16ème conférence internationale. C'est la deuxième fois seulement depuis sa création que l'ICVG se réunit en France et la première fois en Bourgogne, terre de vigne et de vins.
Le Comité de direction de l'ICVG œuvre depuis sa création pour promouvoir les recherches sur ces maladies de dépérissement de la vigne qui déprécient insidieusement les productions des meilleurs cépages dans leur qualité et leur rendement. Que le nombre de participants à ces conférences ne cesse de croître est un gage du succès de son entreprise. Vous découvrirez ici le nombre et la qualité des présentations scientifiques du cru 2009 de l'ICVG. Merci à tous ceux qui y ont contribué et aux partenaires et sponsors qui l'ont grandement aidé.
Bienvenue en Bourgogne et Bienvenue dans ces pages!

FOREWORD

We are very happy that the choice of the Steering Committee of ICVG was turned towards Dijon for the venue of its 16th international conference. This is only the second time since its foundation that ICVG meets in France, the first time in Burgundy, a land of vineyards and wines.
From its very early days, the Steering committee of ICVG has dedicated its efforts to promote research on grapevine decline diseases that insidiously affect the production of best cultivars both in quality and yield. That the number of delegates to conferences steadily increases demonstrates the success of their enterprise. You will discover herein the number and quality of the scientific contributions of vintage 2009 of ICVG. Thanks to all who contributed and to partners and sponsors who greatly helped.
Welcome in Burgundy and Welcome within these pages!

Title : 16th Meeting of the International Council for the Study of Virus and virus-like diseases of the Grapevine – Extended abstracts

Editor : Elisabeth Boudon-Padieu

Publisher : Le Progrès Agricole et Viticole - ISSN 0369-8173

Correct citation

Extended abstracts 16th Meeting of ICVG, Dijon, France, 31 Aug-4 Sept 2009, (pg) – (pg)

REMERCIEMENTS
Nous remercions le Conseil régional de Bourgogne et son président M. le Sénateur François Patriat, pour son soutien financier à l'organisation de la conférence et son hospitalité dans sa salle de conférence.
Nous sommes très redevables à la Communauté de l'Agglomération Dijonnaise (Comadi) en la personne de son président, M. François Rebsamen, Sénateur Maire de Dijon, et de ses collaborateurs pour avoir accepté de mettre à notre disposition pendant trois jours les magnifiques installations du Grand Dijon et toutes les facilités d'accueil d'une assemblée aussi nombreuse.
Nous voulons ici remercier Monsieur Olivier Le Gall, Chef du département Santé des plantes et
Environnement de l'INRA, pour le soutien accordé par le département, et Monsieur Jacques Caneill, président du Centre INRA de Dijon ainsi que Madame Vivienne Gianninazzi-Pearson, Directrice de l'Unité de recherches Plante Microbe Environnement INRA – CNRS – Université de Bourgogne à Dijon, pour nous avoir accordé l'hospitalité de la logistique et du secrétariat indispensables à la préparation de cette conférence.
La publication des Actes n'aurait pu se faire sans la confiance de la Chaire Unesco Culture et traditions du Vin de l'Université de Bourgogne, en la personne de Madame le Professeur Jocelyne Pérard.
Au sein du Comité d'organisation chacun a joué une partie importante dans une atmosphère cordiale et enthousiaste.
Enfin le soutien des organisations et entreprises viticoles de Bourgogne et de Franche-Comté : Bureau
Interprofessionnel des Vins de Bourgogne, Chambre d'Agriculture de Saône et Loire, Société de Viticulture du Jura, Pépinières Guillaume, Domaine Latour, nous a été acquis sans réserve. Qu'elles soient toutes remerciées, en particulier pour leur accueil durant les visites techniques.
Merci aux entreprises Bioreba, Sediag et Bayer Crop Protection qui ont manifesté leur intérêt pour la vaste audience internationale que constitue notre conférence, à la SNCF Gare de Dijon et à l'Office de tourisme de la ville de Dijon qui ont contribué à l'accueil de nos visiteurs proches et lointains.

ACKNOWLEDGEMENTS
We thank the Regional Council of Burgundy and its president, the Senator François Patriat, for their financial support to the organisation of the conference and their hospitality in the Conference Hall.
We are most indebted to the Communauté de l'Agglomération Dijonnaise (Comadi), to its president, Senator and Mayor of Dijon François Rebsamen, and its collaborators for having let us the disposal during three days of the beautiful hall of the Grand Dijon and all facilities necessary to welcome such a large assembly.
We want to thank here Dr. Olivier Le Gall, Head of the Department Plant health and Environment of INRA for the support given by the Department, Dr Jacques Caneill, president of the INRA Centre of Dijon, and Dr. Vivienne Gianninazzi-Pearson, Head of the Research Unit Plant Microbe Environment INRA – CNRS – Université de Bourgogne in Dijon, for hosting the logistics and secretary necessary for the organisation of the Conference
Publication of the Extended Abstracts would not have been possible without the confidence of the Unesco
Chair Culture and Traditions of Wine of University of Burgundy, in the person of its Head, Mrs the Professor Jocelyne Pérard.
Every one in the Organisation committee has played its part with an enthusiastic and hearty complicity. Profession and industry of viticulture of Burgundy and Franche-Comté : Bureau Interprofessionnel des Vins de
Bourgogne, Chambre d'Agriculture de Saône et Loire, Société de Viticulture du Jura, Pépinières Guillaume, Domaine Latour, have fully supported us. We are most thankful to them all, especially for their reception during technical visits.
Bioreba, Sediag and Bayer Crop Protection have readily shown their interest towards the vast international audience of our conference. The SNCF Gare de Dijon and Tourism Office of Dijon city have contributed to the welcome of our visitors from near and remote countries.

Content - Sommaire

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Partners and sponsors – Partenaires et parrainage ICVG Steering Committee – ICVG XVI Organisation Foreword – Avant propos Acknowledgements - Remerciements Content - Sommaire

Session I - Introductory keynotes

  • Oral
  • Martelli G. P.

Grapevine Virology Highlights 2006-09
15

24

Gugerli P.

25 years of serological identification of grapevine leafroll-associated viruses: antiserum and monoclonal

antibodies to GLRaV-1 to GLRaV- 9

  • Dolja V. V.
  • 29

New developments in understanding gene functions and evolution of the grapevine Closteroviruses

Session II – Detection – Plant material and Virus source

Oral

Invited lecture

Sabanadzovic S.
32 36
Viruses of native Vitis germplasm in the Southeastern united states Comparison of High Throughput Low Density Arrays, Rt-PCR and Real-Time Taqman® RT-PCR in the detection of grapevine viruses

Osman F., C. Leutenegger, D.A. Golino, A. Rowhani

Grapevine viruses in Chile: Multi-parallel detection based on metagenomic strategies

Engel E. A., P. F. Escobar, P. Rivera, P. D.T. Valenzuela.

38

40

Grapevine virus collection at Nyon: A contribution to a putative network of a worldwide grapevine virus

reference collection

Gugerli P., J-J. Brugger, M-E. Ramel, S. Besse.

Poster 01 Poster 02

Poster 03

Grapevine virus Q: The first plant virus with a permuted active site of RNA-dependent RNA polymerase

Sabanadzovic S., N. Abou Ghanem-Sabanadzovic, A. E. Gorbalenya

42

44 46
Production of monoclonal antibodies to Grapevine leafroll- associated virus 9 (GLRaV-9)

Gugerli P., S. Rigotti, M-E. Ramel, N. Habili, A. Rowhani, W. Bitterlin, S. Besse.

Detection of viruses in seeds of infected grapevines with an emphasis on Grapevine rupestris stem pitting-

associated virus

Habili N., R. Davies, J. Randles.

Poster 04 Poster 05
Real time PCR for sensitive reliable grapevine virus detection

Malan S., M-J. Freeborough, J. Burger

48

  • 50
  • Prevalence of seven grapevine viruses in table grapes from Vinalopó (Alicante) determined by ELISA and

Real-Time RT-PCR

Bertolini E., C. Martínez, J. García, J. Juárez, A. Martínez, E. Vidal, A. Yuste, M. Albiach-Martí, M. Cambra, A. Olmos.

Poster 06 Poster 07
Virus-derived sequences in the nuclear genome of grapevine

Bertsch C., M. Beuve, V. V. Dolja, M. Wirth, F. Pelsy, E. Herrbach, O. Lemaire

52

  • 54
  • How widespread is the presence of Grapevine leafroll-associated virus 8 (GLRaV-8) putative capsid protein

gene sequences in DNA and RNA obtained from grapevine varieties?

Esteves F., M. Teixeira Santos, M. De Lurdes Rocha, J. E. Eiras-Dias, F. Fonseca

Poster 08 Poster 09 Poster 10
The occurrence of viruses in the clonal selection vineyards in Czech republic

Holleinová V., L. Bláhová, K. Baránková

56 58 60
Contribution of new certified clones to the improvement of the italian table grape industry

La Notte P., C. Pirolo, P. Giannini, G. Bottalico, A. Campanale, V. Savino, G. P. Martelli

Clonal selection and sanitary status of local grapevine germplasm in Serbia

Mandi B., Ž. Ivanovi, L. Susca, G. Bottalico, M. Starovi, D. Jakši, S. Kuzmanovi, D. Ivaniševi, V. Gavrilovi, Kora N., Digiaro M., P. La Notte

Progrès Agricole et Viticole, 2009, Hors Série – Extended abstracts 16th Meeting of ICVG, Dijon, France, 31 Aug – 4 Sept 2009

  • Poster 11
  • Old grapevine varieties vineyards: a window over a pre sanitary selection era and a source of viruses

Teixeira Santos M, M. De Lurdes Rocha, A. Guedes Da Silva, F. Esteves, F. Fonseca, J. E. Eiras-Dias

62

Session III - Fanleaf and other spherical viruses

Oral

Invited lecture

Demangeat G.
64 69
Nepovirus transmission by Longidoridae nematodes with special emphasis on the pair Grapevine fanleaf

virus/Xiphinema index

Identification of plasmodesmata located receptors involved in the movement of Grapevine fanleaf virus (GFLV) and other viruses employing tubule-guided movement

Amari K., E. Boutant, C. Hofmann, L. Fernandes-Calvino, C. Schmitt-Keichinger, P. Didier, C. Thomas, A. Lerich, M. Heinlein, Y. Mély, A. Maule, C. Ritzenthaler

Symptom determinants on the Arabis mosaic nepovirus genome

Dupuis L., C. Himber, P. Dunoyer, A. Bassler, M. Keller, T. Wetzel

71

  • 73
  • Recombination events in Rna-2 of Grapevine fanleaf virus and Arabis mosaic virus in grapevines affected by

Yellow mosaic

Jawhar J., A. Minafra, P. La Notte, C. Pirolo, P. Saldarelli, D. Boscia, V. Savino, G. P. Martelli

The specificity of GFLV and ARMV transmission by their respective nematodes: from structure to function
75

Schellenberger P., G. Demangeat, P. Andret-Link, C. Keichinger, M. Bergdoll, P. Bron, S. Trapani, B. Lorber, C. Sauter, A. Marmonier, D. Esmenjaud, O. Lemaire, M. Fuchs, C. Ritzenthaler

Partial RNA-2 Sequence of Grapevine Bulgarian latent virus

Elbeaino T., F. Fallanaj, M. Digiaro, S. Kuzmanovi

77 79 81
Characterization of Raspberry bushy dwarf virus isolates from grapevine

Mavri Pleško I., M. Viršek-Marn, S. Širca, G. Urek

Isolation of movement protein gene by the use of degenerate primers from Iran isolates of Grapevine fanleaf virus and assessment of the genetic diversity

Sokhandan Bashir N., A. Delpasand Khabbazi

Poster 12 Poster 13 Poster 14

Real-time PCR of Grapevine fanleaf virus

Bláhová L., M. Pidra

83 85 86
First records of Arabis mosaic virus (ARMV) on grapevine in Spain

Abelleira A., J. P. Mansilla, V. Padilla, I. Hita, C. Cabaleiro, A. Olmos, F. J. Legorburu

Absolute quantification of Grapevine fanleaf virus in Chenopodium quinoa using real-time RT-PCR assays

Ulloa S., C. Ritzenthaler, P.D.T. Valenzuela , C. Bruno

Detection of Virus like particles (Vlps) by ISEM in transgenic grapevines expressing different GFLV CP- constructs

  • Poster 15
  • 88

Gottschamel J., M. Castellano, F. Maghuly , M. Laimer

Poster 16 Poster 17
Distribution of Grapevine fanleaf virus (GFLV) in grapevines during the season

epin U., S. Krsmanovi, M. Pompe-Novak, M. Ravnikar

90

  • 92
  • Comparisons of genomic and pathological features among barley and grapevine infecting-isolates of Arabis

mosaic virus

Marmonier A., E. Vigne, V. Komar, G. Demangeat, S. Besse, P. Gugerli, O. Lemaire

  • Poster 18
  • Nicotiana benthamiana plants expressing viral small interfering RNA show differential resistance level

against GFLV
94

Bruno C., P.D.T. Valenzuela

Poster 19 Poster 20
Genetic diversity of the coat protein gene of Chilean isolates of Grapevine fanleaf virus

Zamorano A., A.M. Pino, N Fiore

96

  • 98
  • Genetic variability within the coat protein gene of Grapevine fanleaf virus (GFLV) isolates from South

Africa

Liebenberg A., M-J. Freeborough, C. J Visser, D.U. Bellstedt, J.T. Burger

Poster 21 Poster 22
Mycorrhiza reduce development of the nematode vector of Grapevine fanleaf virus in soil and root systems

Hao Z., L. Fayolle, D. Van Tuinen, X. Li, V. Gianinazzi-Pearson, S. Gianinazzi

100

  • 102
  • Evidence of recombination in 2A gene from a Grapevine fanleaf virus isolate

Nourinejhad Zarghani S., M. Shams-Bakhsh, M. Pazhohande, N. Sokhandan Bashir

Session IV – Epidemiology – Survey of vineyards

  • Oral
  • Development and validation of sampling strategies for the detection of endemic viruses of australian

grapevines

Constable F., P. Nicholas, N. Nancarrow, B. Rodoni

104

  • 106
  • Preliminary results on the quantification of different grapevine viruses in a typical northwestern italian

cultivar

Pacifico D., P. Caciagli, F. Mannini, F. Veratti, C. Marzachi’

Current status of grapevine viruses in the pacific northwest vineyards of the united states

Rayapati N.A., M.A. Tefera, A..J. Olufemi, J. Sridhar, K. Gandhi, L.R. Gutha, R.R. Martin

108 110 112
Survey of wild grapes, weed and cover crop species for grapevine viruses

Golino D.A., S.T. Sim, F. Osman, R. Aldamrat, V. Klaassen, A. Rowhani

Contrasting epidemiologies of grapevine viruses depending on appellation and variety.

Legorburu F.J., E. Recio, E. López, M. Larreina, F. Aguirrezábal, J.F. Cibriaín, R. González-Rodríguez, C. Cabaleiro

Poster 23 Poster 24
A preliminary survey of grapevine viruses in kurdistan province (West of Iran)

Afsharifar A.R., M. Kamali, B. Harighi, S. Bahrami Kamangar, V. Roumi, K. Izadpanah

114

  • 116
  • Occurrence of grapevine leafroll-associated virus-1 and 3 in Croatian autochton grapevine varieties from

Dalmatia

Voncina D., E. Dermic, B. Cvjetkovic, E. Maletic, I. Pejic, J. Karoglan Kontic

Poster 25 Poster 26 Poster 27 Poster 28
Survey of major grapevine virus diseases in the vineyard of Valais (Switzerland)

Besse S., P. Gugerli

118 120 122 124
A survey of grapevine viruses in native cultivars in old plantations of tefneti – Argevineyard, România

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    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/173701 A2 19 November 2015 (19.11.2015) P O P C T (51) International Patent Classification: Not classified HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (21) International Application Number: MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PCT/IB2015/053373 PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (22) International Filing Date: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 8 May 2015 (08.05.2015) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (30) Priority Data: TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 61/991,754 12 May 2014 (12.05.2014) US TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 62/149,893 20 April 2015 (20.04.2015) US DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 62/15 1,013 22 April 2015 (22.04.2015) US LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (71) Applicant: GLAXOSMITHKLINE INTELLECTUAL GW, KM, ML, MR, NE, SN, TD, TG).
  • Serendipitous Identification of a New Iflaviruslike Virus Infecting Tomato, and Its Subsequent Characterisation

    Serendipitous Identification of a New Iflaviruslike Virus Infecting Tomato, and Its Subsequent Characterisation

    Article Type : Original Article Title Page Serendipitous identification of a new Iflavirus-like virus infecting tomato, and its subsequent characterisation. M. Saqib*1,2, S. J. Wylie2, M. G. K. Jones2 Article 1Plant Gene Regulation Research Group, Bioproduction Research Institute. National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan. 2Plant Virus Section, Plant Biotechnology Research Group, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, W.A. 6150, Australia. *Corresponding author Fax: + 61 8 9360 2502 Phone: + 61 8 9360 2424 E mail address: [email protected] Other contact details: [email protected] This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/ppa.12293 Accepted This article is protected by copyright. All rights reserved. [email protected] Running title: Tomato matilda virus from tomato Keywords: picornavirus-like, insect virus, plant virus New abbreviation: tomato matilda virus (TMaV). Abstract The genomic sequence of a previously undescribed virus was identified from symptomless Article tomato plants (Solanum lycopersicum). The viral genome is a positive sense ssRNA molecule of 8,506 nucleotides. It is predicted to encode a single polyprotein of 314.5 kDa, which is subsequently processed into three coat protein components of 13.7, 17.9 and 13.5 kDa, and a viral replicase of approximately 207 kDa with conserved motifs for a helicase, a protease, and RNA-dependent RNA polymerase (RdRp).
  • Plant Virus–Host Interaction Molecular Approaches and Viral Evolution

    Plant Virus–Host Interaction Molecular Approaches and Viral Evolution

    Plant Virus–Host Interaction Molecular Approaches and Viral Evolution R.K. Gaur Associate Professor and Head, Department of Science, FASC, Mody Institute of Technology and Science, Lashmangarh, Sikar, India Thomas Hohn Professor Emeritus, Botanical Institute, University of Basel, Basel, Switzerland Pradeep Sharma Senior Scientist (Biotechnology), Directorate of Wheat Research, Karnal, India AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier The Boulevard, Langford Lane, Kidlington, Oxford, OX5 1GB, UK 225 Wyman Street, Waltham, MA 02451, USA First published 2014 Copyright © 2014 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangement with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein.
  • Molecular Characterization of Novel Soybean-Associated Viruses Identified by High-Throughput Sequencing

    Molecular Characterization of Novel Soybean-Associated Viruses Identified by High-Throughput Sequencing

    CORE Metadata, citation and similar papers at core.ac.uk Provided by Illinois Digital Environment for Access to Learning and Scholarship Repository MOLECULAR CHARACTERIZATION OF NOVEL SOYBEAN-ASSOCIATED VIRUSES IDENTIFIED BY HIGH-THROUGHPUT SEQUENCING BY TUBA YASMIN THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Crop Sciences in the Graduate College of the University of Illinois at Urbana-Champaign, 2016 Urbana, Illinois Master’s Committee: Associate Professor Leslie L. Domier, adviser Associate Professor Kristopher N. Lambert Professor Glen L. Hartman ABSTRACT High-throughput sequencing of mRNA from soybean leaf samples collected from North Dakota and Illinois soybean fields revealed the presence of two novel soybean-associated viruses. The first virus has a single-stranded positive-sense RNA genome consisting of 8,693 nt that contains two large open reading frames (ORFs). The predicted amino acid sequence of the first ORF showed similarity to structural proteins, of members of the invertebrate-infecting Dicistroviridae and the sequence of the second ORF which is a nonstructural proteins lack affinity to other virus sequences available in GenBank. The presence of separate ORFs for the structural and nonstructural proteins was similar to members of the family Dicistroviridae, but the order of the two ORFs in the new virus was opposite to that of the family Dicistroviridae. Because of the virus’ unique genome organization and the lack of strong phylogenetic association with previously described virus families, the soybean-associated virus may represent a novel virus family. The second virus also has a single stranded positive sense RNA genome, but has two genomic segments.
  • Untranslated Region of Bean Pod Mottle Virus RNA2 Is

    Untranslated Region of Bean Pod Mottle Virus RNA2 Is

    Journal of General Virology (2013), 94, 1415–1420 DOI 10.1099/vir.0.051755-0 Short A stem–loop structure in the 59 untranslated region Communication of bean pod mottle virus RNA2 is specifically required for RNA2 accumulation Junyan Lin,1 Ahmed Khamis Ali,1,3 Ping Chen,1,4 Said Ghabrial,5 John Finer,2 Anne Dorrance,1 Peg Redinbaugh1,6 and Feng Qu1 Correspondence 1Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio Feng Qu State University, 1680 Madison Ave, Wooster, OH 44691, USA [email protected] 2Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691, USA 3Department of Biology, College of Science, University of Mustansiriyah, Bagdad, Iraq 4Key Laboratory of Protection and Utilization of Tropical Crop Germplasm Resources, Hainan University, Haikou, Hainan, People’s Republic of China 5Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA 6USDA-ARS, Corn and Soybean Research Unit, Wooster, OH 44691, USA Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus of the family Secoviridae. Its RNA1 encodes all proteins needed for genome replication and is capable of autonomous replication. By contrast, BPMV RNA2 must utilize RNA1-encoded proteins for replication. Here, we sought to identify RNA elements in RNA2 required for its replication. The exchange of 59 untranslated regions (UTRs) between genome segments revealed an RNA2- specific element in its 59 UTR. Further mapping localized a 66 nucleotide region that was predicted to fold into an RNA stem–loop structure, designated SLC.
  • An Evolutionary Analysis of the Secoviridae Family of Viruses

    An Evolutionary Analysis of the Secoviridae Family of Viruses

    An Evolutionary Analysis of the Secoviridae Family of Viruses Jeremy R. Thompson1*, Nitin Kamath1,2, Keith L. Perry1 1 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America, 2 Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America Abstract The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.2961023 to 2.7461023 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies.
  • From Infection to Healing: the Use of Plant Viruses in Bioactive Hydrogels

    From Infection to Healing: the Use of Plant Viruses in Bioactive Hydrogels

    Received: 4 February 2020 Revised: 8 June 2020 Accepted: 23 June 2020 DOI: 10.1002/wnan.1662 ADVANCED REVIEW From infection to healing: The use of plant viruses in bioactive hydrogels Christina Dickmeis | Louisa Kauth | Ulrich Commandeur Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Abstract Germany Plant viruses show great diversity in shape and size, but each species forms unique nucleoprotein particles that are symmetrical and monodisperse. The Correspondence Christina Dickmeis, Institute for genetically programed structure of plant viruses allows them to be modified by Molecular Biotechnology, RWTH Aachen genetic engineering, bioconjugation, or encapsulation to form virus University, Aachen, Germany. nanoparticles (VNPs) that are suitable for a broad range of applications. Plant Email: christina.dickmeis@molbiotech. rwth-aachen.de VNPs can be used to present foreign proteins or epitopes, to construct inor- ganic hybrid materials, or to carry molecular cargos, allowing their utilization Funding information as imaging reagents, immunomodulators, therapeutics, nanoreactors, and bio- Deutsche Forschungsgemeinschaft, Grant/ Award Number: 654127; RWTH Aachen sensors. The medical applications of plant viruses benefit from their inability University to infect and replicate in human cells. The structural properties of plant viruses also make them useful as components of hydrogels for tissue engineering. Hydrogels are three-dimensional networks composed of hydrophilic polymers that can absorb large amounts of water. They are used as supports for tissue regeneration, as reservoirs for controlled drug release, and are found in contact lenses, many wound healing materials, and hygiene products. They are also useful in ecological applications such as wastewater treatment. Hydrogel-based matrices are structurally similar to the native extracellular matrix (ECM) and provide a scaffold for the attachment of cells.

  • Tobacco Ringspot Virus

    Bulletin OEPP/EPPO Bulletin (2017) 47 (2), 135–145 ISSN 0250-8052. DOI: 10.1111/epp.12376 European and Mediterranean Plant Protection Organization Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes PM 7/2 (2) Diagnostics Diagnostic PM 7/2 (2) Tobacco ringspot virus Specific scope Specific approval and amendment This Standard describes a diagnostic protocol for Tobacco First approved in 2000-09. ringspot virus1 Revision approved in 2017-03 This Standard should be used in conjunction with PM 7/76 Use of EPPO diagnostic protocols. A flow diagram describing the procedure for detection 1. Introduction and identification of TRSV is given in Fig. 1. Tobacco ringspot virus (TRSV) is the type member of the genus Nepovirus within the family Secoviridae. It has isomet- 2. Identity ric particles of approximately 28 nm and is readily transmit- Name: Tobacco ringspot virus ted by sap inoculation. It is transmitted in nature by the Synonym: Anemone necrosis virus, blueberry necrotic ring- nematode vector Xiphinema americanum and closely related spot virus Xiphinema species. Thrips tabaci, spider mites, grasshoppers Taxonomic position: Viruses: Picornovirales: Secoviridae: and aphids have also been reported as possible vectors (Stace- Comovirinae: Secoviridae: Nepovirus Smith, 1985) but their significance for the natural spread of EPPO Code: TRSV00 TRSV is currently unclear. The same holds true for Apis Phytosanitary categorization: EPPO A2 List no. 228; EU mellifera (the European honeybee), in which TRSV was Annex I/A1 found to systemically spread and propagate (Li et al., 2014). TRSV is transmitted by seed in several host plants. It naturally 3.