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Requirements for the Packaging of Geminivirus Circular Single-Stranded DNA: Effect of DNA Length and Coat Protein Sequence
viruses Article Requirements for the Packaging of Geminivirus Circular Single-Stranded DNA: Effect of DNA Length and Coat Protein Sequence Keith Saunders 1,* , Jake Richardson 2, David M. Lawson 1 and George P. Lomonossoff 1 1 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; [email protected] (D.M.L.); george.lomonossoff@jic.ac.uk (G.P.L.) 2 Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-1603-450733 Received: 10 September 2020; Accepted: 28 October 2020; Published: 30 October 2020 Abstract: Geminivirus particles, consisting of a pair of twinned isometric structures, have one of the most distinctive capsids in the virological world. Until recently, there was little information as to how these structures are generated. To address this, we developed a system to produce capsid structures following the delivery of geminivirus coat protein and replicating circular single-stranded DNA (cssDNA) by the infiltration of gene constructs into plant leaves. The transencapsidation of cssDNA of the Begomovirus genus by coat protein of different geminivirus genera was shown to occur with full-length but not half-length molecules. Double capsid structures, distinct from geminate capsid structures, were also generated in this expression system. By increasing the length of the encapsidated cssDNA, triple geminate capsid structures, consisting of straight, bent and condensed forms were generated. The straight geminate triple structures generated were similar in morphology to those recorded for a potato-infecting virus from Peru. -
Data Sheet on Cowpea Mild Mottle 'Carlavirus'
Prepared by CABI and EPPO for the EU under Contract 90/399003 Data Sheets on Quarantine Pests Cowpea mild mottle 'carlavirus' IDENTITY Name: Cowpea mild mottle 'carlavirus' Taxonomic position: Viruses: Possible Carlavirus Common names: CPMMV (acronym) Angular mosaic (of beans), pale chlorosis (of tomato) (English) Notes on taxonomy and nomenclature: CPMMV is serologically closely related to groundnut crinkle, psophocarpus necrotic mosaic, voandzeia mosaic and tomato pale chlorosis viruses and is probably synonymous with them (Jeyanandarajah & Brunt, 1993). It is not serologically related to known carlaviruses, and should possibly be placed in a new sub-group of the carlaviruses. EPPO computer code: CPMMOX EU Annex designation: I/A1 HOSTS Natural hosts include Canavalia ensiformis, groundnuts (Arachis hypogaea), Phaseolus lunatus, P. vulgaris, Psophocarpus tetragonolobus, soyabeans (Glycine max), tomatoes (Lycopersicon esculentum), Vigna mungo, probably aubergines (Solanum melongena), cowpeas cv. Blackeye (Vigna unguiculata), Vicia faba and Vigna subterranea. The virus also occurs in various weeds (Fabaceae), including Stylosanthes and Tephrosia spp. Many more hosts can be artificially inoculated. GEOGRAPHICAL DISTRIBUTION EPPO region: Egypt, Israel. Asia: India (Karnataka, Maharashtra and probably elsewhere), Indonesia, Israel, Malaysia, Thailand, Yemen. Africa: Côte d'Ivoire, Egypt, Ghana, Kenya, Malawi, Mozambique, Nigeria, Sudan, Tanzania, Togo, Uganda, Zambia. South America: Brazil. Oceania: Fiji, Papua New Guinea, Solomon Islands. EU: Absent. BIOLOGY Unlike carlaviruses in general, CPMMV is transmitted in a non-persistent manner (Jeyanandarajah & Brunt, 1993). The ability to transmit CPMMV is usually retained for a maximum of 20-60 min (Muniyappa & Reddy, 1983). Non-vector transmission is by mechanical inoculation. Seed transmission has been demonstrated in a number of hosts in different countries, but there are also negative reports. -
Autographa Gamma
1 Table of Contents Table of Contents Authors, Reviewers, Draft Log 4 Introduction to the Reference 6 Soybean Background 11 Arthropods 14 Primary Pests of Soybean (Full Pest Datasheet) 14 Adoretus sinicus ............................................................................................................. 14 Autographa gamma ....................................................................................................... 26 Chrysodeixis chalcites ................................................................................................... 36 Cydia fabivora ................................................................................................................. 49 Diabrotica speciosa ........................................................................................................ 55 Helicoverpa armigera..................................................................................................... 65 Leguminivora glycinivorella .......................................................................................... 80 Mamestra brassicae....................................................................................................... 85 Spodoptera littoralis ....................................................................................................... 94 Spodoptera litura .......................................................................................................... 106 Secondary Pests of Soybean (Truncated Pest Datasheet) 118 Adoxophyes orana ...................................................................................................... -
P. Lava Kumar, A. T. Jones and F. Waliyar
Methods Manual Edited by P. Lava Kumar, A. T. Jones and F. Waliyar Virology and Mycotoxin Diagnostics Laboratory International Crops Research Institute for the Semi-Arid Tropics © International Crops Research Institute for the Semi-Arid Tropics, 2004 AUTHORS P. LAVA KUMAR Special Project Scientist – Virology Virology and Mycotoxin Diagnostics ICRISAT, Patancheru 502 324, India e-mail: [email protected] A. T. JONES Senior Principal Virologist Scottish Crop Research Institute (SCRI) Invergowrie Dundee DD2 5DA Scotland, United Kingdom e-mail: [email protected] FARID WALIYAR Principal Scientist and Global Theme Leader – Biotechnology ICRISAT, Patancheru 502 324, India e-mail: [email protected] Material from this manual may be reproduced for the research use providing the source is acknowledged as: KUMAR, P.L., JONES, A. T. and WALIYAR, F. (Eds) (2004). Serological and nucleic acid based methods for the detection of plant viruses. International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 324, India. FOR FURTHER INFORMATION: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru - 502 324, Andhra Pradesh, India Telephone: +91 (0) 40 23296161 Fax: +91 (0) 40 23241239 +91 (0) 40 23296182 Web site: http://www.icrisat.org Cover photo: Purified particles of PoLV-PP (©Kumar et al., 2001) This publication is an output from the United Kingdom Department for International Development (DFID) Crop Protection Programme for the benefit of developing countries. Views expressed are not necessarily those of DFID. Manual designed by P Lava Kumar Serological and Nucleic Acid Based Methods for the Detection of Plant Viruses Edited by P. -
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: 2016.021a-kP officers) Short title: Establishment of a family of single-stranded DNA satellites with two genera (e.g. 6 new species in the genus Zetavirus) Modules attached 2 3 4 5 (modules 1 and 11 are required) 6 7 8 9 10 Author(s): R.W. Briddon, J. Navas-Castillo and E. Fiallo-Olivé on behalf of the Geminiviridae SG Corresponding author with e-mail address: [email protected], [email protected], [email protected] 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 subcommittee Geminiviridae SG chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) ICTV Study Group comments (if any) and response of the proposer: Date first submitted to ICTV: August 2016 Date of this revision (if different to above): ICTV-EC comments and response of the proposer: Page 1 of 17 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. -
Recovery Plan for Cowpea Mild Mottle Virus, a Seedborne Carlavirus (?) Judith K. Brown School of Plant Sciences University of A
Recovery Plan for Cowpea mild mottle virus, a seedborne carla-like virus Judith K. Brown School of Plant Sciences University of Arizona, Tucson and Jose Carlos Verle Rodrigues University of Puerto Rico, San Juan NPDRS meeting APS, Minneapolis-Saint Paul, MN August 10, 2014 Cowpea mild mottle virus (CpMMV) Origin (endemism): Africa: Kenya (1957), Ghana (1973)* Host: groundnut Arachis hypogaea L (1957, 1997, Sudan) cowpea Vigna unguiculata L. (1973) Distribution: now, worldwide in all legume growing locales (27+ documented) but importance in soybean unrealized until recently. Transmission •Whitefly-transmitted in non-persistent manner; Bemisia tabaci (Genn.) sibling species group (Muniyappa, 1983) AAP 10 min, IAP 5 min •Mechanically transmissible, experimentally •Seed borne to varying extents in different species and varieties of same species; particularly severe in certain soybean varieties. *often cited as the first report because the disease went largely unnoticed until then Likely multiple strains, but largely uninvestigated Synonyms: Groundnut crinkle (Dubern and Dollet, 1981) Psophocarpus necrotic mosaic (Fortuner et al., 1979) Voandzeia mosaic (Fauquet and Thouvenel, 1987) in the Cote d'Ivoire, tomato pale chlorosis in Israel (Cohen & Antignus, 1982) Tomato fuzzy vein in Nigeria (Brunt & Phillips, 1981) Bean angular mosaic virus in Brazil (Costa et al., 1983; Gaspar et al., 1985) shown to be serologically most closely related to CPMMV = proposed, distinct strains Isolates from solanaceous hosts in Jordan and Israel, although very similar to West African and Indian legume isolates, considered to be distinct strains – more information needed to confirm and differentiate (Menzel et al., 2010). Wide variation in virulence of CPMMV isolates from other countries also reported (Anno-Nyako, 1984, 1986, 1987; Siviprasad and Sreenivasulu, 1996). -
Cowpea Mild Mottle Virus Infecting Soybean Crops in Northwestern Argentina
Cowpea mild mottle virus Infecting Soybean Crops in Northwestern Argentina Irma G. Laguna, Joel D. Arneodo, Patricia Rodríguez-Pardina & Magdalena Fiorona Instituto de Fitopatología y Fisiología Vegetal, Instituto Nacional de Tecnología Agropecuaria - INTA, Camino 60 Cuadras km 5½, X5020ICA Córdoba, Argentina, e-mail:[email protected] (Accepted for publication on 20/01/2006) Corresponding autor: Irma G. Laguna RESUMO Cowpea mild mottle virus infectando soja no noroeste da Argentina Relata-se a ocorrência natural do Cowpea mild mottle virus (CPMMV, gênero Carlavirus) em culturas de soja [Glycine max (L.) Merr.] na província de Salta (noroeste argentino). Argentina is one of the leading soybean producing observed in samples from asymptomatic soybeans. On and exporting countries in the world. During the 2004/2005 this basis, plants were tested for Cowpea mild mottle virus cropping season, soybean production reached a record (CPMMV, genus Carlavirus) by DAS-ELISA. Leaf samples �8.� million tons. Although soybean is grown mainly in were ground in extraction buffer (PBS pH 6.8 + 0.05% Tween the central Pampas, it is also cultivated in the northwest 20 + 2% polyvinyl pyrrolidone) at a 1:5 (w/v) dilution. of the country, where it plays a significant role in the local Specific polyclonal antisera (DSMZ GmbH, Germany) were economy. Among the biotic factors affecting soybean used. Positive (supplied by DSMZ) and negative (healthy yields in this region, fungal diseases account for the major soybean) controls were included on each microtitre plate. economic losses (Wrather et al., Plant Dis. 81:107. 1997). After incubation with p-nitrophenyl phosphate at room Nevertheless, diseases of viral etiology have also been temperature for 1 h, A405nm values greater than 0.�00 were recorded. -
Characterization, Phylogeny and Recombination Analysis of Pedilanthus Leaf Curl Virus-Petunia Isolate and Its Associated Betasat
Shakir et al. Virology Journal (2018) 15:134 https://doi.org/10.1186/s12985-018-1047-y RESEARCH Open Access Characterization, phylogeny and recombination analysis of Pedilanthus leaf curl virus-Petunia isolate and its associated betasatellite Sara Shakir1,3, Muhammad Shah Nawaz-ul-Rehman1*, Muhammad Mubin1 and Zulfiqar Ali2 Abstract Background: Geminiviruses cause major losses to several economically important crops. Pedilanthus leaf curl virus (PeLCV) is a pathogenic geminivirus that appeared in the last decade and is continuously increasing its host range in Pakistan and India. This study reports the identification and characterization of PeLCV-Petunia from ornamental plants in Pakistan, as well as geographical, phylogenetic, and recombination analysis. Methods: Viral genomes and associated satellites were amplified, cloned, and sequenced from Petunia atkinsiana plants showing typical geminivirus infection symptoms. Virus-satellite complex was analyzed for phylogenetic and recombination pattern. Infectious clones of isolated virus and satellite molecules were constructed using a partial dimer strategy. Infectivity analysis of PeLCV alone and in combination with Digera yellow vein betasatellite (DiYVB) was performed by Agrobacterium infiltration of Nicotiana benthamiana and Petunia atkinsiana plants with infectious clones. Results: PeLCV, in association with DiYVB, was identified as the cause of leaf curl disease on P. atkinsiana plants. Sequence analysis showed that the isolated PeLCV is 96–98% identical to PeLCV from soybean, and DiYVB has 91% identity to a betasatellite identified from rose. Infectivity analysis of PeLCV alone and in combination with DiYVB, performed by Agrobacterium infiltration of infectious clones in N. benthamiana and P. atkinsiana plants, resulted in mild and severe disease symptoms 14 days after infiltration, respectively, demonstrating that these viruses are natural disease-causing agents. -
Emergence of a New Cucurbit-Infecting Begomovirus Species Capable of Forming Viable Reassortants with Related Viruses in the Squash Leaf Curl Virus Cluster J
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Papers in Plant Pathology Plant Pathology Department 3-13-2002 Emergence of a New Cucurbit-Infecting Begomovirus Species Capable of Forming Viable Reassortants with Related Viruses in the Squash leaf curl virus Cluster J. K. Brown University of Arizona, [email protected] A. M. Idris University of Arizona C. Alteri University of Arizona Drake C. Stenger University of Nebraska-Lincoln Follow this and additional works at: http://digitalcommons.unl.edu/plantpathpapers Brown, J. K.; Idris, A. M.; Alteri, C.; and Stenger, Drake C., "Emergence of a New Cucurbit-Infecting Begomovirus Species Capable of Forming Viable Reassortants with Related Viruses in the Squash leaf curl virus Cluster" (2002). Papers in Plant Pathology. 284. http://digitalcommons.unl.edu/plantpathpapers/284 This Article is brought to you for free and open access by the Plant Pathology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Papers in Plant Pathology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Virology Emergence of a New Cucurbit-Infecting Begomovirus Species Capable of Forming Viable Reassortants with Related Viruses in the Squash leaf curl virus Cluster J. K. Brown, A. M. Idris, C. Alteri, and Drake C. Stenger First, second, and third authors: Department of Plant Sciences, University of Arizona, Tucson 85721; and fourth author: USDA-ARS and Department of Plant Pathology, University of Nebraska, Lincoln 68583. Accepted for publication 13 March 2002. ABSTRACT Brown, J. K., Idris, A. M., Alteri, C., and Stenger, D. C. 2002. Emergence virus-R (SLCV-R), SLCV-E, and Bean calico mosaic virus (BCaMV) at of a new cucurbit-infecting begomovirus species capable of forming 84, 83, and 80%, respectively. -
Checkv Assesses the Quality and Completeness of Metagenome-Assembled Viral Genomes
ARTICLES https://doi.org/10.1038/s41587-020-00774-7 CheckV assesses the quality and completeness of metagenome-assembled viral genomes Stephen Nayfach 1 ✉ , Antonio Pedro Camargo 2, Frederik Schulz 1, Emiley Eloe-Fadrosh 1, Simon Roux1 and Nikos C. Kyrpides 1 ✉ Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the com- pleteness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates complete- ness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and com- parison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions. iruses are the most abundant biological entity on Earth, a uniform length threshold (for example 5 or 10 kb) and -
Metagenomic Analysis of the Begomovirus Diversity in Tomatoes in Central Brazil and Impact of the Ty-1 Tolerance Gene on Viral Evolutionary Dynamics
Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Fitopatologia Doctoral Thesis Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics LUCIANE DE NAZARÉ ALMEIDA DOS REIS Brasília - DF 2020 LUCIANE DE NAZARÉ ALMEIDA DOS REIS Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Phytopathology by the Post-Graduate Program in Phytopathology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Leonardo Silva Boiteux BRASÍLIA, DF– BRASIL 2020 FICHA CATALOGRÁFICA Reis, A. N. L. Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics Luciane de Nazaré Almeida dos Reis. Brasília, 2020. Pages number p.:205 Doctoral Thesis - Programa de Pós-Graduação em Fitopatologia, Universidade de Brasília, Brasília, DF. I- Tomato, NGS, Geminiviridae, Begomovirus, Genomoviridae. II- Universidade de Brasília. PPG/FIT. III- Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics Aos meus pais Eliecê Almeida dos Reis e Lucival Nunes dos Reis. Ao meu irmão Luan Almeida dos Reis. Aos meus avós Deusarina Goes Almeida e Ubiratan Nascimento Almeida (In memorian). Ao meu Amor Gustavo Ribeiro Dedico Agradecimentos A Deus, dono de toda a ciência, sabedoria e poder. -
Evidence That Whitefly-Transmitted Cowpea Mild Mottle Virus Belongs To
Arch Virol (1998) 143: 769–780 Evidence that whitefly-transmitted cowpea mild mottle virus belongs to the genus Carlavirus 1 2 2 2; 1 R. A. Naidu ,S.Gowda , T. Satyanarayana , V. Boyko ∗, A. S. Reddy , W. O. Dawson2, and D. V. R. Reddy1 1Crop Protection Division, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India 2Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, Florida, U.S.A. Accepted October 7,1997 Summary. Two strains of whitefly-transmitted cowpea mild mottle virus (CP- MMV) causing severe (CPMMV-S) and mild (CPMMV-M) disease symptoms in peanuts were collected from two distinct agro-ecological zones in India. The host-range of these strains was restricted to Leguminosae and Chenopodiaceae, and each could be distinguished on the basis of symptoms incited in different hosts. The 30-terminal 2500 nucleotide sequence of the genomic RNA of both the strains was 70% identical and contains five open reading frames (ORFs). The first three (P25, P12 and P7) overlap to form a triple gene block of proteins, P32 en- codes the coat protein, followed by P12 protein located at the 30 end of the genome. Genome organization and pair-wise comparisons of amino acid sequences of pro- teins encoded by these ORFs with corresponding proteins of known carlaviruses and potexviruses suggest that CPMMV-S and CPMMV-M are closely related to viruses in the genus Carlavirus. Based on the data, it is concluded that CPMMV is a distinct species in the genus Carlavirus. Introduction Cowpea mild mottle virus (CPMMV) was first reported on cowpea in Ghana [3].