Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses
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Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses
viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. -
Sobemovirus Coat Protein Gene Complements Long-Distance Movement of a Coat Protein-Null Dianthovirus
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Virology 330 (2004) 186–195 www.elsevier.com/locate/yviro A Sobemovirus coat protein gene complements long-distance movement of a coat protein-null Dianthovirus Anton S. Callaway1, Carol G. George, Steven A. Lommel* Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, United States Received 16 August 2004; returned to author for revision 9 September 2004; accepted 28 September 2004 Abstract Red clover necrotic mosaic virus (RCNMV; genus Dianthovirus) and Turnip rosette virus (TRoV; genus Sobemovirus) are taxonomically and ecologically distinct plant viruses. In addition, the two genera differ in the role of coat protein (CP) in cell-to-cell movement. However, both are small icosahedral viruses requiring CP for systemic movement in the host vasculature. Here, we show that the TRoV CP gene is capable of facilitating the vascular movement of a Dianthovirus. Substitution of the RCNMV CP gene with the TRoV CP gene permits movement of the resulting chimeric virus to non-inoculated leaves. RCNMV lacking a CP gene or containing a non-translatable TRoV CP gene do not move systemically. This report introduces the molecular characterization of TRoV and describes the unprecedented complementation of systemic movement function by intergenic complete substitution of a plant virus CP gene. D 2004 Elsevier Inc. All rights reserved. Keywords: Long-distance movement; Complementation; Coat protein; Dianthovirus; Sobemovirus; Arabidopsis; Chimera Introduction sal and encapsidation is not sufficient for long-distance movement of some viruses (Callaway et al., 2001; Sit et The mechanism(s) by which plant viruses move through al., 2001). -
In Track Changes Mode
Archives of Virology: Brief Reports Cymbidium chlorotic mosaic virus, a new sobemovirus isolated from the spring orchid (Cymbidium goeringii) in Japan Hideki Kondo*, Shogo Takemoto, Kazuyuki Maruyama, Sotaro Chiba**, Ida Bagus Andika and Nobuhiro Suzuki Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan *Corresponding author: Hideki Kondo Tel. +81(86) 434-1232; Fax. +81(86) 434-1232 e-mail: [email protected] ** Present address, Asia Satellite Campus Institute, The Graduate School of Agricultural Science, Nagoya University, Nagoya 464-8601 Japan Running Title: Characterization of Cymbidium chlorotic mosaic virus 1 Abstract Cymbidium chlorotic mosaic virus (CyCMV), isolated from a spring orchid (Cymbidium goeringii), was characterized molecularly. CyCMV isometric virions comprise a single, positive-strand RNA genome of 4,083 nucleotides and 30-kDa coat protein. The virus genome potentially encodes for five overlapping open reading frames with a similar genomic organization to sobemoviruses. BLAST searches and phylogenetic analyses revealed that CyCMV is most closely related to papaya lethal yellowing virus, a proposed dicot-infecting sobemovirus (58.8% nucleotide sequence identity), but has a relatively distant relationship to monocot-infecting sobemoviruses, with only modest sequence identities. These suggest that CyCMV is a new monocot-infecting member of the floating genus Sobemovirus. Main text Cymbidium is one of the most commercially important cultivated orchids (Orchidaceae), comprising nearly 52 species that are widely distributed in the tropical and subtropical regions of Asia [6]. Cymbidium mosaic virus (CymMV, genus Potexvirus), odontoglossum ringspot virus (ORSV, genus Tobamovirus) and orchid fleck virus (proposed genus Dichorhavirus) are the most prevalent and economically important Cymbidium infecting viruses [1, 3]. -
Structure of Native and Expanded Sobemoviruses by Electron Cryo-Microscopy and Image Reconstruction
doi:10.1006/jmbi.2000.4043 available online at http://www.idealibrary.com on J. Mol. Biol. (2000) 303, 197±211 Structure of Native and Expanded Sobemoviruses by Electron Cryo-Microscopy and Image Reconstruction Natacha Opalka1,2, Mariana Tihova2, Christophe Brugidou3 Abhinav Kumar4, Roger N. Beachy1, Claude M. Fauquet3 and Mark Yeager2,4,5* 1Division of Plant Biology Rice yellow mottle virus (RYMV) and southern bean mosaic virus, cowpea strain (SCPMV) are members of the Sobemovirus genus of RNA- 2Department of Cell Biology containing viruses. We used electron cryo-microscopy (cryo-EM) and 3International Laboratory for icosahedral image analysis to examine the native structures of these two Tropical Agricultural viruses at 25 AÊ resolution. Both viruses have a single tightly packed Biotechnology (ILTAB/ capsid layer with 180 subunits assembled on a T 3 icosahedral lattice. ORSTOM-TSRI), Division of Distinctive crown-like pentamers emanate from the 12 5-fold axes of Plant Biology symmetry. The exterior face of SCPMV displays deep valleys along the 4 2-fold axes and protrusions at the quasi-3-fold axes. While having a Department of Molecular similar topography, the surface of RYMV is comparatively smooth. Two Biology, The Scripps Research concentric shells of density reside beneath the capsid layer of RYMV and Institute, 10550 North Torrey SCPMV, which we interpret as ordered regions of genomic RNA. In the Pines Road, La Jolla presence of divalent cations, SCPMV particles swell and fracture, whereas CA 92037, USA the expanded form of RYMV is stable. We previously proposed that the 5Scripps Clinic, Division of cell-to-cell movement of RYMV in xylem involves chelation of Ca2 from Cardiovascular Diseases, 10666 pit membranes of infected cells, thereby stabilizing the capsid shells and North Torrey Pines Road, La allowing a pathway for spread of RYMV through destabilized Jolla, CA 92037, USA membranes. -
An Annotated List of Plant Viruses and Viroids Described in Brazil (1926-2018)
Biota Neotropica 20(2): e20190932, 2020 www.scielo.br/bn ISSN 1676-0611 (online edition) Inventory An annotated list of plant viruses and viroids described in Brazil (1926-2018) Elliot W. Kitajima1* 1Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Fitopatologia e Nematologia, 13418-900, Piracicaba, SP, Brasil *Corresponding author: Elliot W. Kitajima, e-mail: [email protected] KITAJIMA, E.W. An annotated list of plant viruses and viroids described in Brazil (1926-2018). Biota Neotropica 20(2): e20190932. https://doi.org/10.1590/1676-0611-BN-2019-0932. Abstract: A list of plant species, in alphabetical order by their scientific name, and the viruses found naturally infecting them in Brazilian territory, with some comments, was prepared . The production of such a list was based on a yearly catalog of publications on plant viruses collected by the author, from 1926 to 2018. Listed species of viruses were those recognized by the International Committee on Taxonomy of Viruses (ICTV), but also those characterized and still waiting official recognition, were included. Several cases of putative viral diseases were listed for historical reasons expecting to raise interest for their clarification. This list includes 345 plants species belonging to 74 families naturally infected by plant viruses in Brazil. Fabaceae and Asteraceae had most virus- infected species, respectively 49 and 36. Until 2018, a total of 213 plant virus and 6 viroid species belonging to 57 genera and 22 families and 6 orders, officially recognized by ICTV, were found naturally infecting these plants. Begomovirus and Potyvirus genera have most representatives, with 45 and 42 species, respectively. -
Viruses: Do Plant Viruses Evolve Differently from the Others? Cecile Desbiez, Benoît Moury, Hervé Lecoq
The hallmarks of “green” viruses: do plant viruses evolve differently from the others? Cecile Desbiez, Benoît Moury, Hervé Lecoq To cite this version: Cecile Desbiez, Benoît Moury, Hervé Lecoq. The hallmarks of “green” viruses: do plant viruses evolve differently from the others?. Infection, Genetics and Evolution, Elsevier, 2011, 11 (5), pp.812-824. 10.1016/j.meegid.2011.02.020. hal-02652387 HAL Id: hal-02652387 https://hal.inrae.fr/hal-02652387 Submitted on 29 May 2020 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. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License Version définitive du manuscrit publié dans / Final version of the manuscript published in : Infection, Genetics and Evolution, 2011,11, 812-824. The original publication is available at http://www.sciencedirect.com/science/article/pii/S1567134811000621. DOI: 10.1016/j.meegid.2011.02.020. The hallmarks of “green” viruses: do plant viruses evolve differently from the others? Desbiez C, Moury B, Lecoq H INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France Corresponding author : [email protected] 1. Introduction 2. Taxonomy of plant viruses and relation to viruses infecting other hosts 3. -
Complete Sections As Applicable
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.011aP officers) Short title: Create species Imperata yellow mottle virus in the genus Sobemovirus (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Drissa Sérémé ([email protected]), Sévérine Lacombe, Moumouni Konaté, Agnès Pinel- Galzi, Valentin Stanislas Edgar Traoré, Eugénie Hébrard, Oumar Traoré, Christophe Brugidou, Denis Fargette, Gnissa Konaté List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . If in doubt, contact the appropriate Sobemovirus Study Group subcommittee chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) ICTV-EC or Study Group comments and response of the proposer: Date first submitted to ICTV: 15 August 2011 Date of this revision (if different to above): Page 1 of 6 MODULE 2: NEW SPECIES Creating and naming one or more new species. If more than one, they should be a group of related species belonging to the same genus. -
A Novel RNA Virus Related to Sobemoviruses Confers Hypovirulence on the Phytopathogenic Fungus Sclerotinia Sclerotiorum
Article A Novel RNA Virus Related to Sobemoviruses Confers Hypovirulence on the Phytopathogenic Fungus Sclerotinia sclerotiorum Ayesha Azhar 1,2, Fan Mu 1,2, Huang Huang 1,2, Jiasen Cheng 1,2, Yanping Fu 2, Muhammad Rizwan Hamid 1,2, Daohong Jiang 1,2 and Jiatao Xie 1,2,* 1 State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China 2 Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China * Correspondence author: [email protected] Received: 16 May 2019; Accepted: 15 August 2019; Published: 16 August 2019 Abstract: Infection by diverse mycoviruses is a common phenomenon in Sclerotinia sclerotiorum. In this study, the full genome of a single-stranded RNA mycovirus, tentatively named Hubei sclerotinia RNA virus 1 (HuSRV1), was determined in the hypovirulent strain 277 of S. sclerotiorum. The HuSRV1 genome is 4492 nucleotides (nt) long and lacks a poly (A) tail at the 3ˊ- terminus. Sequence analyses showed that the HuSRV1 genome contains four putative open reading frames (ORFs). ORF1a was presumed to encode a protein with a conserved protease domain and a transmembrane domain. This protein is 27% identical to the P2a protein encoded by the subterranean clover mottle virus. ORF1b encodes a protein containing a conserved RNA-dependent RNA polymerase (RdRp) domain, which may be translated into a fusion protein by a -1 ribosome frameshift. This protein is 45.9% identical to P2b encoded by the sowbane mosaic virus. ORF2 was found to encode a putative coat protein, which shares 23% identical to the coat protein encoded by the olive mild mosaic virus. -
Hypera Postica) and Its Host Plant, Alfalfa (Medicago Sativa
Article Characterisation of the Viral Community Associated with the Alfalfa Weevil (Hypera postica) and Its Host Plant, Alfalfa (Medicago sativa) Sarah François 1,2,*, Aymeric Antoine-Lorquin 2, Maximilien Kulikowski 2, Marie Frayssinet 2, Denis Filloux 3,4, Emmanuel Fernandez 3,4, Philippe Roumagnac 3,4, Rémy Froissart 5 and Mylène Ogliastro 2,* 1 Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Park Road, Oxford OX1 3SY, UK 2 DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE 34095 Montpellier, France; [email protected] (A.A.-L.); [email protected] (M.K.); [email protected] (M.F.) 3 CIRAD, UMR PHIM, 34090 Montpellier, France; [email protected] (D.F.); [email protected] (E.F.); [email protected] (P.R.) 4 PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD 34090 Montpellier, France 5 MIVEGEC Infectious and Vector Diseases: Ecology, Genetics, Evolution and Control, University of Montpellier, CNRS, IRD 34394 Montpellier, France; [email protected] Citation: François, S.; * Correspondence: [email protected] (S.F.); [email protected] (M.O.) Antoine-Lorquin, A.; Kulikowski, M.; Frayssinet, M.; Abstract: Advances in viral metagenomics have paved the way of virus discovery by making the Filloux, D.; Fernandez, E.; exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach Roumagnac, P.; Froissart, R.; opens new possibilities to explore how viruses circulate between insects and plants, which may help Ogliastro, M. Characterisation of the to optimise their management. It could also lead to identifying novel entomopathogenic viral re- Viral Community Associated with sources potentially suitable for biocontrol strategies. -
Encyclopedia of Plant Viruses and Viroids K
Encyclopedia of Plant Viruses and Viroids K. Subramanya Sastry • Bikash Mandal John Hammond • S. W. Scott R. W. Briddon Encyclopedia of Plant Viruses and Viroids K. Subramanya Sastry Bikash Mandal Indian Council of Agricultural Indian Agricultural Research Institute Research, IIHR New Delhi, India Bengaluru, India Indian Council of Agricultural Research, IIOR and IIMR Hyderabad, India John Hammond S. W. Scott USDA, Agricultural Research Service Clemson University Beltsville, MD, USA Clemson, SC, USA R. W. Briddon John Innes Centre Norwich, UK ISBN 978-81-322-3911-6 ISBN 978-81-322-3912-3 (eBook) ISBN 978-81-322-3913-0 (print and electronic bundle) https://doi.org/10.1007/978-81-322-3912-3 # Springer Nature India Private Limited 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. -
Supplementary Materials
Supplementary materials Figure S1. The predicted transmembrane helix domain of polyprotein P1a (according to TMHMM server 2.0). Figure S2. Two-sided view of the predicted 3D structure of CP of HuSRV1 (Phyre2). Each chain of CP is represented by a different color: Chain A, red; Chain B, green; and Chain C, blue. Small light green beads indicate the position of Ca2+ binding sites (UCSF Chimera). Viruses 2019, 11, x; doi: FOR PEER REVIEW www.mdpi.com/journal/viruses Viruses 2019, 11, x FOR PEER REVIEW 2 of 4 Figure S3. Evolutionary relationship of the protease of Hubei sclerotinia RNA virus 1 (highlighted in blue) with other viruses of the genera Sobemovirus, Polerovirus, Enamovirus, and Barnavirus. The number on branches indicates results of analyses of 1000 bootstrap replicates. The bar at lower left quarter represents the genetic distance. Accession number of viruses used for phylogenetic analysis was listed in Table S2. Table S1. The list of the primers used in the study. Primer Name Sequence HuSRV1-F1 5′-CTGCTGTCGGTTCTTCAAC-3' HuSRV1-R1 5′-ACATTCAGCCTACCAGACG-3' HuSRV1-F2 5′-CTGCTGTCGGTTCTTCAAC-3' HuSRV1-R2 5′-ACATTCAGCCTACCAGACG-3' RACE-3RT/ Random dN6 5'-CGATCGATCATGATGCAATGCNNNNNN-3' primer 5′pGGATCCCGGGAATTCGGTAATACGACTCACTATATTTTTATA PC3-T7 Loop adapter GTGAGTCGTATTA-OH-3ˊ PC2 primer 5′-p-CCGAATTCCCGGGATCC-3′ Seq. specific primer - 5end 5′-AGTGCTTTGACACCGAGAAC-3′ HuSRV1-5end-R1 Seq. specific primer - 5end 5′-GCCAGTACCAATCGAAAGAG-3′ HuSRV1-5end-R2 Seq. specificprimer - 3end 5′-CCGCAACAACACTGTCACTGG-3′ HuSRV1-3end-F1 Seq. specific primer -3end 5′-GGTAATGCTAGCGGCAACACTG-3′ HuSRV1-3end-F2 SsMTV1-F 5′-CGAGCCATTCCCCGATACA-3′ SsMTV1-R 5′-GAGTCCTGACCAATGAGTGCTG-3′ Viruses 2019, 11, x FOR PEER REVIEW 3 of 4 Table S2. -
Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present
Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present Denis Fargette1*, Agne`s Pinel-Galzi1, Drissa Se´re´me´ 2,Se´verine Lacombe3, Euge´nie He´brard1, Oumar Traore´ 2, Gnissa Konate´ 2 1 Institut de Recherche pour le De´veloppement (IRD), UMR RPB, Montpellier, France, 2 Institut de l’Environnement et de Recherches Agricoles (INERA), Laboratoire de Biotechnologie et de Virologie Ve´ge´tale, Kamboinse´, Ouagadougou, Burkina Faso, 3 Institut de Recherche pour le De´veloppement (IRD), UMR GDP, Montpellier, France Abstract The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between sobemoviruses and poleroviruses approximately 5,000 years, and that among sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation.