Disruption of Virus Movement Confers Broad-Spectrum Resistance Against
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Comparative Analysis, Distribution, and Characterization of Microsatellites in Orf Virus Genome
www.nature.com/scientificreports OPEN Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome Basanta Pravas Sahu1, Prativa Majee 1, Ravi Raj Singh1, Anjan Sahoo2 & Debasis Nayak 1* Genome-wide in-silico identifcation of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036–1,181 microsatellites per strain. The further screening revealed the presence of 83–107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6–8.4 and 53.0–59.5 bp/ kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6–0.8 and 12.1–17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD signifcantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-signifcantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)- x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. -
The Occurrence of the Viruses in Narcissus L
Journal of Horticultural Research 2016, vol. 24(2): 19-24 DOI: 10.1515/johr-2016-0016 _______________________________________________________________________________________________________ THE FREQUENCY OF VIRAL INFECTIONS ON TWO NARCISSUS PLANTATIONS IN CENTRAL POLAND Short communication Dariusz SOCHACKI1*, Ewa CHOJNOWSKA2 1Warsaw University of Life Sciences – SGGW, Nowoursynowska 166, 02-767 Warsaw, Poland 2Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice Received: November 2016; Accepted: December 2016 ABSTRACT Viral diseases in narcissus can drastically affect yields and quality of narcissus bulbs and flowers, leading even to a total crop loss. To test the frequency of viral infections in production fields in Central Poland, samples were collected over three years from two cultivars and two plantations, and tested for the presence of Arabis mosaic (ArMV), Cucumber mosaic (CMV), Narcissus latent (NLV), Narcissus mosaic (NMV) and the potyvirus group using the Enzyme Linked ImmunoSorbent Assay. Potyviruses, NLV and NMV were detected in almost all leaf samples in both cultivars, in all three years of testing. Other viruses were detected in a limited number of samples. In most cases mixed infections were present. Tests on bulbs have shown the presence of potyviruses and NMV, with the higher number of positives in cultivar ‘Carlton’. In addition, for most viruses an increase in their detectability was observed on both plantations in subse- quent seasons. Key words: ELISA, flower bulbs, negative selection, viral disease INTRODUCTION (NMV). Many of the most important viruses infect- ing narcissus belongs to the potyvirus group. Viral diseases can drastically affect yield as Asjes (1996) reported that degeneration of nar- well as quality of narcissus bulbs and flowers, some- cissus plants caused by viruses may decrease bulb times resulting in a total crop loss. -
Comparison of Plant‐Adapted Rhabdovirus Protein Localization and Interactions
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2011 COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS Kathleen Marie Martin University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Martin, Kathleen Marie, "COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS" (2011). University of Kentucky Doctoral Dissertations. 172. https://uknowledge.uky.edu/gradschool_diss/172 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Kathleen Marie Martin The Graduate School University of Kentucky 2011 COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Kathleen Marie Martin Lexington, Kentucky Director: Dr. Michael M Goodin, Associate Professor of Plant Pathology Lexington, Kentucky 2011 Copyright © Kathleen Marie Martin 2011 ABSTRACT OF DISSERTATION COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS Sonchus yellow net virus (SYNV), Potato yellow dwarf virus (PYDV) and Lettuce Necrotic yellows virus (LNYV) are members of the Rhabdoviridae family that infect plants. SYNV and PYDV are Nucleorhabdoviruses that replicate in the nuclei of infected cells and LNYV is a Cytorhabdovirus that replicates in the cytoplasm. LNYV and SYNV share a similar genome organization with a gene order of Nucleoprotein (N), Phosphoprotein (P), putative movement protein (Mv), Matrix protein (M), Glycoprotein (G) and Polymerase protein (L). -
Diversity of Plant Virus Movement Proteins: What Do They Have in Common?
processes Review Diversity of Plant Virus Movement Proteins: What Do They Have in Common? Yuri L. Dorokhov 1,2,* , Ekaterina V. Sheshukova 1, Tatiana E. Byalik 3 and Tatiana V. Komarova 1,2 1 Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; [email protected] (E.V.S.); [email protected] (T.V.K.) 2 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia 3 Department of Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; [email protected] * Correspondence: [email protected] Received: 11 November 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of single-stranded RNA in a non-sequence-specific manner, (b) participation in the intracellular trafficking of genomic RNA to the plasmodesmata (Pd), and (c) localization in Pd and enhancement of Pd permeability, have been used as a reference in the search and analysis of candidate proteins from other plant viruses. Nevertheless, although almost four decades have passed since the introduction of the term “movement protein” into scientific circulation, the mechanism underlying its function remains unclear. It is unclear why, despite the absence of homology, different MPs are able to functionally replace each other in trans-complementation tests. Here, we consider the complexity and contradictions of the approaches for assessment of the ability of plant viral proteins to perform their movement function. -
Cellular and Molecular Aspects of Rhabdovirus Interactions with Insect and Plant Hosts∗
ANRV363-EN54-23 ARI 23 October 2008 14:4 Cellular and Molecular Aspects of Rhabdovirus Interactions with Insect and Plant Hosts∗ El-Desouky Ammar,1 Chi-Wei Tsai,3 Anna E. Whitfield,4 Margaret G. Redinbaugh,2 and Saskia A. Hogenhout5 1Department of Entomology, 2USDA-ARS, Department of Plant Pathology, The Ohio State University-OARDC, Wooster, Ohio 44691; email: [email protected], [email protected] 3Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; email: [email protected] 4Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506; email: [email protected] 5Department of Disease and Stress Biology, The John Innes Centre, Norwich, NR4 7UH, United Kingdom; email: [email protected] Annu. Rev. Entomol. 2009. 54:447–68 Key Words First published online as a Review in Advance on Cytorhabdovirus, Nucleorhabdovirus, insect vectors, virus-host September 15, 2008 interactions, transmission barriers, propagative transmission The Annual Review of Entomology is online at ento.annualreviews.org Abstract This article’s doi: The rhabdoviruses form a large family (Rhabdoviridae) whose host ranges 10.1146/annurev.ento.54.110807.090454 include humans, other vertebrates, invertebrates, and plants. There are Copyright c 2009 by Annual Reviews. at least 90 plant-infecting rhabdoviruses, several of which are economi- by U.S. Department of Agriculture on 12/31/08. For personal use only. All rights reserved cally important pathogens of various crops. All definitive plant-infecting 0066-4170/09/0107-0447$20.00 and many vertebrate-infecting rhabdoviruses are persistently transmit- Annu. Rev. Entomol. 2009.54:447-468. -
An Insect Nidovirus Emerging from a Primary Tropical Rainforest
RESEARCH ARTICLE An Insect Nidovirus Emerging from a Primary Tropical Rainforest Florian Zirkel,a,b,c Andreas Kurth,d Phenix-Lan Quan,b Thomas Briese,b Heinz Ellerbrok,d Georg Pauli,d Fabian H. Leendertz,c W. Ian Lipkin,b John Ziebuhr,e Christian Drosten,a and Sandra Junglena,c Institute of Virology, University of Bonn Medical Center, Bonn, Germanya; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USAb; Research Group Emerging Zoonosesc and Center for Biological Safety-1,d Robert Koch Institute, Berlin, Germany; and Institute of Medical Virology, Justus Liebig University Gießen, Gießen, Germanye ABSTRACT Tropical rainforests show the highest level of terrestrial biodiversity and may be an important contributor to micro- bial diversity. Exploitation of these ecosystems may foster the emergence of novel pathogens. We report the discovery of the first insect-associated nidovirus, tentatively named Cavally virus (CAVV). CAVV was found with a prevalence of 9.3% during a sur- vey of mosquito-associated viruses along an anthropogenic disturbance gradient in Côte d’Ivoire. Analysis of habitat-specific virus diversity and ancestral state reconstruction demonstrated an origin of CAVV in a pristine rainforest with subsequent spread into agriculture and human settlements. Virus extension from the forest was associated with a decrease in virus diversity (P < 0.01) and an increase in virus prevalence (P < 0.00001). CAVV is an enveloped virus with large surface projections. The RNA genome comprises 20,108 nucleotides with seven major open reading frames (ORFs). ORF1a and -1b encode two large pro- teins that share essential features with phylogenetically higher representatives of the order Nidovirales, including the families Coronavirinae and Torovirinae, but also with families in a basal phylogenetic relationship, including the families Roniviridae and Arteriviridae. -
Synthesis of Potato Virus X Rnas by Membrane- Containing Extracts
JOURNAL OF VIROLOGY, July 1996, p. 4795–4799 Vol. 70, No. 7 0022-538X/96/$04.0010 Copyright q 1996, American Society for Microbiology Synthesis of Potato Virus X RNAs by Membrane- Containing Extracts SERGEY V. DORONIN AND CYNTHIA HEMENWAY* Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622 Received 16 October 1995/Accepted 30 March 1996 Membrane-containing extracts isolated from tobacco plants infected with the plus-strand RNA virus, potato virus X (PVX), supported synthesis of four major, high-molecular-weight PVX RNA products (R1 to R4). Nuclease digestion and hybridization studies indicated that R1 and R2 are a mixture of partially single- stranded replicative intermediates and double-stranded replicative forms. R3 and R4 are double-stranded products containing sequences typical of the two major PVX subgenomic RNAs. The newly synthesized RNAs were demonstrated to have predominantly plus-strand polarity. Synthesis of these products was remarkably stable in the presence of ionic detergents. Potato virus X (PVX), the type member of the Potexvirus tracts were derived from Nicotiana tabacum leaves at 7 days genus, is a flexuous rod-shaped particle containing a single, postinoculation by a procedure similar to that described by genomic RNA of 6.4 kb that is capped and polyadenylated (21, Lurie and Hendrix (15). Inoculated and upper leaves (50 g) 27). Of the five open reading frames (ORFs), the first encodes were homogenized in 150 ml of buffer I (50 mM Tris-HCl [pH a 165-kDa protein (P1) that has homology to other known 7.5], 250 mM sucrose, 5 mM MgCl2, 1 mM EDTA, 10 mM RNA-dependent RNA polymerase (RdRp) proteins (23). -
Nucleotide Sequence and Phylogenetic Analysis of a Bamboo Mosaic Potexvirus Isolate from Common Bamboo (Bambusa Vulgaris Mcclure)
YangBot. Bull. et al. Acad. Nucleotide Sin. (1997) sequence 38: 77-84 of BaMV-V RNA 77 Nucleotide sequence and phylogenetic analysis of a bamboo mosaic potexvirus isolate from common bamboo (Bambusa vulgaris McClure) Chi-Chen Yang1,2, Jih-Shiou Liu1, Chan-Pin Lin2 and Na-Sheng Lin1,3 1Institute of Botany, Academia Sinica, Taipei, Taiwan 115, Republic of China 2Department of Plant Pathology and Entomology, National Taiwan University, Taipei, Taiwan, Republic of China (Received September 20, 1996; Accepted January 30, 1997) Abstract. The complete cDNA sequence corresponding to the genomic RNA of an isolate bamboo mosaic potexvirus (BaMV-V) from common bamboo (Bambusa vulgaris McClure) was determined. This isolate is the first potexvirus with which a satellite RNA has been associated. The genome organization of BaMV-V, similar to those of other potexviruses, contained five open reading frames (ORFs 15) coding for polypeptides with molecular weight of 156 kDa, 28 kDa, 13 kDa, 6 kDa, and 25 kDa, respectively. Nucleotide sequence analysis showed a 10.0% difference from the BaMV-O isolate previously described whereas the amino acid comparison showed a difference of 3.2%. When three conservative domains of RNA dependent RNA polymerase (RdRp) were used for phylogenetic analysis, the greatest variation between two strains of each virus was only 12.8% of that between the two closest members of the potexvirus group. The grouping of potexviruses distinct from other groups of plant viruses was also confirmed by a comparision of three conservative motifs of RdRp. Keywords: Bamboo mosaic virus; Nucleotide sequence; Potexvirus. Introduction virus M, PVM) (Zavriev et al., 1991), hordeivirus (e.g. -
Tamada-Text R3 HK-TT
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Okayama University Scientific Achievement Repository Tamada & Kondo - 1 Journal of General Plant Pathology Biological and genetic diversity of plasmodiophorid-transmitted viruses and their vectors Tetsuo Tamada* and Hideki Kondo Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan. Current address for T. Tamada: Kita 10, Nishi 1, 13-2-606, Sapporo, 001-0010, Japan. *Corresponding author: Tetsuo Tamada; E-mail: [email protected] Total text pages 32 Word counts: 10 words (title); 147 words (Abstract); 6004 words (Main Text) Tables: 3; Figure: 1; Supplementary figure: 1 Tamada & Kondo - 2 Abstract About 20 species of viruses belonging to five genera, Benyvirus, Furovirus, Pecluvirus, Pomovirus and Bymovirus, are known to be transmitted by plasmodiophorids. These viruses have all positive-sense single-stranded RNA genomes that consist of two to five RNA components. Three species of plasmodiophorids are recognized as vectors: Polymyxa graminis, P. betae, and Spongospora subterranea. The viruses can survive in soil within the long-lived resting spores of the vector. There are biological and genetic variations in both virus and vector species. Many of the viruses have become the causal agents of important diseases in major crops, such as rice, wheat, barley, rye, sugar beet, potato, and groundnut. Control measure is dependent on the development of the resistant cultivars. During the last half a century, several virus diseases have been rapidly spread and distributed worldwide. For the six major virus diseases, their geographical distribution, diversity, and genetic resistance are addressed. -
Virus Diseases of Trees and Shrubs
VirusDiseases of Treesand Shrubs Instituteof TerrestrialEcology NaturalEnvironment Research Council á Natural Environment Research Council Institute of Terrestrial Ecology Virus Diseases of Trees and Shrubs J.1. Cooper Institute of Terrestrial Ecology cfo Unit of Invertebrate Virology OXFORD Printed in Great Britain by Cambrian News Aberystwyth C Copyright 1979 Published in 1979 by Institute of Terrestrial Ecology 68 Hills Road Cambridge CB2 ILA ISBN 0-904282-28-7 The Institute of Terrestrial Ecology (ITE) was established in 1973, from the former Nature Conservancy's research stations and staff, joined later by the Institute of Tree Biology and the Culture Centre of Algae and Protozoa. ITE contributes to and draws upon the collective knowledge of the fourteen sister institutes \Which make up the Natural Environment Research Council, spanning all the environmental sciences. The Institute studies the factors determining the structure, composition and processes of land and freshwater systems, and of individual plant and animal species. It is developing a sounder scientific basis for predicting and modelling environmental trends arising from natural or man- made change. The results of this research are available to those responsible for the protection, management and wise use of our natural resources. Nearly half of ITE's work is research commissioned by customers, such as the Nature Con- servancy Council who require information for wildlife conservation, the Forestry Commission and the Department of the Environment. The remainder is fundamental research supported by NERC. ITE's expertise is widely used by international organisations in overseas projects and programmes of research. The photograph on the front cover is of Red Flowering Horse Chestnut (Aesculus carnea Hayne). -
Alternanthera Mosaic Potexvirus in Scutellaria1 Carlye A
Plant Pathology Circular No. 409 (396 revised) Florida Department of Agriculture and Consumer Services January 2013 Division of Plant Industry FDACS-P-01861 Alternanthera Mosaic Potexvirus in Scutellaria1 Carlye A. Baker2, and Lisa Williams2 INTRODUCTION: Skullcap, Scutellaria species. L. is a member of the mint family, Labiatae. It is represented by more than 300 species of perennial herbs distributed worldwide (Bailey and Bailey 1978). Skullcap grows wild or is naturalized as ornamentals and medicinal herbs. Fuschia skullcap is a Costa Rican variety with long, trailing stems, glossy foliage and clusters of fuschia-colored flowers. SYMPTOMS: Vegetative propagations of fuschia skullcap grown in a Central Florida nursery located in Manatee County showed symptoms of viral infec- tion in the fall of 1998, including foliar mottle and chlorotic to necrotic ring- spots and wavy-line patterns (Fig. 1). SURVEY AND DETECTION: Symptomatic leaves were collected and ex- amined by electron microscopy. Flexuous virus-like particles, approximately 500 nm long, like those associated with potexvirus infections, were observed. Subsequent enzyme-linked immunosorbent assay (ELISA) for a potexvirus known to occur in Florida, resulted in a positive reaction to papaya mosaic virus (PapMV) antiserum. However, further tests indicated that while this virus was related to PapMV, it was not PapMV. Sequencing data showed that the virus was actually Alternanthera mosaic virus (Baker et al. 2006). VIRUS DISTRIBUTION: In 1999, a Potexvirus closely related to PapMY was found in Queensland, Australia. It was isolated from Altrernanthera pugens (Amaranthaceae), a weed found in both the Southern U.S. and Australia. Despite its apparent relationship with PapMV using serology, sequencing Fig. -
The Development and Characterisation of Grapevine Virus-Based
The development and characterisation of grapevine virus-based expression vectors by Jacques du Preez Presented in partial fulfilment of the requirements for the degree Doctor of Philosophy at the Department of Genetics, Stellenbosch University March 2010 Supervisors: Prof JT Burger and Dr DE Goszczynski Study leader: Dr D Stephan Declaration I, the undersigned, hereby declare that the work contained in this thesis is my own original work and that I have not previously in its entirety or in part submitted it at any university for a degree. ______________________ Date: _______________ Jacques du Preez Copyright © 2010 Stellenbosch University All rights reserved ii Abstract Grapevine ( Vitis vinifera L.) is a very important agricultural commodity that needs to be protected. To achieve this several in vivo tools are needed for the study of this crop and the pathogens that infect it. Recently the grapevine genome has been sequenced and the next important step will be gene annotation and function using these in vivo tools. In this study the use of Grapevine virus A (GVA), genus Vitivirus , family Flexiviridae , as transient expression and VIGS vector for heterologous protein expression and functional genomics in Nicotiana benthamiana and V . vinifera were evaluated. Full-length genomic sequences of three South African variants of the virus (GTR11, GTG111 and GTR12) were generated and used in a molecular sequence comparison study. Results confirmed the separation of GVA variants into three groups, with group III (mild variants) being the most distantly related. It showed the high molecular heterogeneity of the virus and that ORF 2 was the most diverse. The GVA variants GTG111, GTR12 and GTR11 were placed in molecular groups I, II and III respectively.