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Zindović J, Čizmović M, Vučurović A, Margaria P, Škorić D. Increased Diversity of Citrus Tristeza Virus in Europe. Plant Dis 2024:PDIS09231718RE. [PMID: 37990525 DOI: 10.1094/pdis-09-23-1718-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
This study investigated the genetic diversity of Citrus tristeza virus (CTV) isolates from Montenegro and Croatia, European countries with the northernmost citrus-growing regions situated on the Eastern Adriatic coast. Fifteen complete or nearly complete CTV genomes were reconstructed by high-throughput sequencing of samples collected in distinct municipalities in Montenegro and Opuzen municipality in Croatia. Phylogenetic analyses assigned some of the sequences to VT and T30 strains, previously recorded in Europe, while remarkably other isolates were placed in S1 and RB groups, which have not been reported in Europe so far. In addition, a new phylogenetic lineage comprising only isolates from Montenegro was delineated and tentatively proposed as the MNE cluster. Recombination analysis revealed evidence of 11 recombination events in the sequences obtained in this study, between isolates of related strains, within isolates of the same strain, and between distant strains. These findings show that CTV diversity in Europe is higher than reported before and calls for the reevaluation of management strategies.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jelena Zindović
- Department for Plant Protection, Biotechnical Faculty, University of Montenegro, 81000 Podgorica, Montenegro
| | - Miroslav Čizmović
- Department for Plant Protection, Biotechnical Faculty, University of Montenegro, 81000 Podgorica, Montenegro
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
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Cultrona M, Bonini N, Margaria P, Menzel W, Pacifico D, Tessitori M. First report of strawberry polerovirus 1 in strawberry in Italy. Plant Dis 2024. [PMID: 38379223 DOI: 10.1094/pdis-01-24-0239-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Strawberry (Fragaria × ananassa Duch.) was introduced in Sicily (Italy) in the 1930s in the small town of Maletto, on the slopes of Etna volcan, where it's currently cultivated in a total area of 30 ha. The French cv. 'Madame Moutot', appreciated for its unique flavor and intense fragrance, was there propagated vegetatively and after decades, the distinctive 'Etna ecotype' originated by adaptation to the peculiar environmental conditions of the area (Milella et al., 2006). In May 2023, in a 0.5 ha "Etna ecotype" strawberry field, virus-like symptoms were observed in approximately 50% of the plants. Symptoms included severe dwarfing, leaf cupping and chlorotic spotting which lead to decline of infected plants. To investigate the etiology of the disease, leaf samples were collected from eight symptomatic plants for analysis by High-Throughput Sequencing (HTS). To this aim, total RNAs were extracted by using the RNeasy PowerPlant Kit (Qiagen, Germany). The RNAs were pooled, depleted of ribosomal RNA (QIAseq FastSelect; Qiagen), and a library was prepared according to the Illumina DNA Prep Kit. Sequencing on a NextSeq2000 instrument at Leibniz Institute DSMZ (Braunschweig, Germany) generated 31,149,784 of paired-end reads (150 nt), which were further analyzed in Geneious Prime version 2023.2 (Biomatters) using a custom workflow for virus discovery and genome assembly. Analysis of the assembled contigs by local BLASTn and BLASTp alignments against a custom plant virus database of NCBI nuclear-core (NC) reference sequences assigned a number of contigs to accession NC_025435, strawberry polerovirus 1 (SPV-1). Reconstruction of the virus genome by assembly of contigs and reads alignment resulted in a nearly complete genome sequence of SPV-1 (GenBank Acc. No. OR989958) showing by BLASTn 98.69% identity to the SPV-1 NC reference sequence, and 98.99 % identity with an isolate from the Czech Republic (GenBank Acc. OL421571). To confirm the presence of SPV-1 in each sample, RT-PCR using specific primers designed in this study SPV-1-CP-1F (5'-TCGAGATACGTCTAGAACTGCAA-3') and SPV-1-CP-1R (5'-GAGAGGCCCCTTCTACCTATTTG-3') targeting the entire 623 bp coat protein (CP) gene was performed. Amplicons of the expected size were obtained in five samples and Sanger-sequenced. The resulting sequences shared 99.85% - 100% of identity to the HTS - derived sequence (GenBank Acc. No. OR989958) through BLASTn analysis. Strawberry mottle virus (SMoV), strawberry mild yellow edge virus (SMYEV) and strawberry crinkle virus (SCV) were detected in the same library in addition to SPV-1 and then confirmed by RT-PCR using specific primers (Martin & Tzanetakis 2013). Strawberry polerovirus 1, related to the genus Polerovirus in the family Solemoviridae, was first reported in strawberries in Canada (Xiang et al. 2015) and was thereafter detected in the United States (Thekke-Veetil & Tzanetakis 2016), Argentina (Luciani et al. 2016), and Nepal (Kuwak et al. 2022). To date, the virus has been reported in Europe only in the Czech Republic (Franova et al. 2021). To our knowledge, this is the first report of SPV-1 in strawberry plants in Italy. Although the correlation between SPV-1 and strawberry decline (SD) is still uncertain (Xiang et al. 2015) transmission of the virus via aphids has recently been demonstrated (Franova et al. 2021). Our report let to hypothesize that its dissemination in Europe can be considered as increasing.
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Affiliation(s)
- Massimiliano Cultrona
- University of Catania, 9298, Department of Agriculture, Food and Environment (Di3A), Via Santa Sofia 100, Catania, Catania, Italy, 95123;
| | - Naomi Bonini
- Università degli Studi di Catania, 9298, Agriculture, Food and Environment (Di3A) , Catania, Italy;
| | - Paolo Margaria
- Leibniz Institut - DMSZ, Plant Virus Department, Messeweg 11-12, Braunschweig, Germany, 38104;
| | - Wulf Menzel
- Leibniz Institute DSMZ, Plant Virus Department, Inhoffenstrasse 7B, Braunschweig, Germany, 38124;
| | - Davide Pacifico
- Consiglio Nazionale delle Ricerche, 9327, Istituto di Bioscienze e Biorisorse, Corso Calatafimi 414, Palermo, Italy, 90129;
| | - Matilde Tessitori
- University of Catania, 9298, Department of Agriculture, Food and Environment (Di3A), Via Santa Sofia, 100, Catania, Italy, 95123;
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Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, Marais A, Candresse T. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol 2023; 97:e0130023. [PMID: 37888981 PMCID: PMC10688312 DOI: 10.1128/jvi.01300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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Affiliation(s)
| | - Oumaima Moubset
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Stephan Winter
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
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Pielhop TP, Popp C, Fricke S, Knierim D, Margaria P, Maiß E. Molecular characterization of two new alternaviruses identified in members of the fungal family Nectriaceae. Arch Microbiol 2023; 205:129. [PMID: 36947239 PMCID: PMC10033562 DOI: 10.1007/s00203-023-03477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/23/2023]
Abstract
Since the first report in 2009, at least ten additional viruses have been identified and assigned to the proposed virus family Alternaviridae. Here we report two new mycoviruses tentatively assigned to this family, both identified as members of the fungal family Nectriaceae, which were isolated from surface-disinfected apple roots (Malus x domestica, Borkh.) affected by apple replant disease (ARD). ARD is a highly complex, worldwide-occurring disease resulting from plant reactions to a disturbed (micro)-biome and leads to high economic losses every year. The first alternavirus characterized in this study was identified in a Dactylonectria torresensis isolate. The virus was tentatively named dactylonectria torresensis alternavirus 1 (DtAV1) as the first member of the proposed new species Alternavirus dactylonectriae. The second virus was identified in an isolate of Ilyonectria robusta and was tentatively named ilyonectria robusta alternavirus 1 (IrAV1) as the first member of the proposed new species Alternavirus ilyonectriae. Full genomic sequences of the viruses were determined and are presented. Further, we found hints for putative components of a methyl transferase machinery using in silico approaches. This putative protein domain is encoded by segment 2. However, this result only establishes the basis for subsequent studies in which the function must be confirmed experimentally in vitro. Thus, this is the first study where a function is predicted to all three genomic segments within the group of the alternaviruses. These findings provide further insights into the virome of ARD-associated fungi and are therefore another brick in the wall of understanding the complexity of the disease.
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Affiliation(s)
- Tom P Pielhop
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Carolin Popp
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Sebastian Fricke
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Dennis Knierim
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Braunschweig, Germany
| | - Paolo Margaria
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Braunschweig, Germany
| | - Edgar Maiß
- Institute of Horticultural Production Systems, Department Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Pielhop TP, Popp C, Knierim D, Margaria P, Maiß E. First report of a chrysovirus infecting a member of the fungal genus Ilyonectria. Arch Virol 2022; 167:2411-2415. [PMID: 35963918 PMCID: PMC9556398 DOI: 10.1007/s00705-022-05551-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]
Abstract
The fungus Ilyonectria pseudodestructans belongs to the family Nectriaceae and was found to be part of the endophytic microbiome of apple trees (Malus x domestica, Borkh.) with apple replant disease (ARD). After dsRNA extraction, a mycoviral infection became evident. Here, we report the identification of a new virus, tentatively named "Ilyonectria pseudodestructans chrysovirus 1" (IpCV1), as the first member of the proposed new species "Alphachrysovirus ilyonectriae" within the genus Alphachrysovirus. This is the first report of a chrysovirus infecting a member of the fungal genus Ilyonectria. IpCV1 has a tripartite dsRNA genome with a total length of 8944 bp. The segments are 3439 bp, 2850 bp, and 2655 bp in length, and each dsRNA carries a single ORF. The encoded viral proteins are a 125.92-kDa RNA-dependent RNA polymerase, a 100.75-kDa coat protein, and one protein of unknown function with a predicted molecular mass of 93.04 kDa. The 5´ and 3´ UTRs are comparatively short and are 79 to 91 bp and 62 to 148 bp in length, respectively. This study provides the basis for further investigations of the impact of IpCV1 on its host and the etiology of ARD.
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Affiliation(s)
- Tom P Pielhop
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Carolin Popp
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Dennis Knierim
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany
| | - Paolo Margaria
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany
| | - Edgar Maiß
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Sareli K, Winter S, Chatzivassiliou EΚ, Knierim D, Margaria P. High molecular diversity of full-length genome sequences of zucchini yellow fleck virus from Europe. Arch Virol 2022; 167:2305-2310. [PMID: 35941394 PMCID: PMC9556397 DOI: 10.1007/s00705-022-05558-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
Abstract
Zucchini yellow fleck virus (ZYFV), genus Potyvirus, is the causal agent of a disease of cucurbits. The genome sequences of seven ZYFV isolates of different origin were determined, two of which were reconstructed from a squash (Cucurbita sp.) collected in 2017 in Greece, while the others, accessions from the DSMZ Plant Virus Collection, were from samples collected in Italy, Greece, and France in the 1980s and 1990s. A high level of molecular diversity, well dispersed along the genome, was observed, but this was within the limits for assignment of the virus isolates to the same species. P1 was the most diverse gene, and isolates from squash contained an insertion in this gene.
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Affiliation(s)
- Kyriaki Sareli
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
- Laboratory of Plant Pathology, Department of Crop Science, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, Athens, Greece
| | - Stephan Winter
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Elisavet Κ Chatzivassiliou
- Laboratory of Plant Pathology, Department of Crop Science, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, Athens, Greece.
| | - Dennis Knierim
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Paolo Margaria
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany.
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Quito-Avila DF, Reyes-Proaño EG, Mendoza A, Margaria P, Menzel W, Bera S, Simon AE. Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador. Arch Virol 2022; 167:2093-2098. [PMID: 35821148 DOI: 10.1007/s00705-022-05525-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
Abstract
Two new umbravirus-like associated RNAs (ulaRNAs) were found, respectively, in maize and Johnsongrass samples from Ecuador. The complete sequences consist of 3,053 and 3,025 nucleotides, respectively, and contain four open reading frames (ORFs). Their genome sequences were 58% identical to each other and 28 to 60% identical to the most closely related viruses. Phylogenetic analysis using full genome sequences and amino acid sequence of the RNA-dependent-RNA polymerase (RdRp) placed both sequences in a clade sharing the most recent common ancestor with ulaRNAs from sugarcane and maize, suggesting that they belong to a monophyletic grass-infecting lineage. Their terminal regions exhibit features common to umbraviruses and ulaRNAs.
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Affiliation(s)
- Diego F Quito-Avila
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador. .,Centro de Investigaciones Biotecnológicas del Ecuador, CIBE, Escuela Superior Politécnica del Litoral, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador.
| | - Edison G Reyes-Proaño
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Km 30.5 Vía Perimetral Campus Gustavo Galindo, Guayaquil, Ecuador
| | - Alma Mendoza
- INIAP, Estación Experimental Portoviejo, Km 12, Via a Santa Ana, Manabí, Ecuador
| | - Paolo Margaria
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, Braunschweig, Germany
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20742, USA
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20742, USA
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Mendoza AR, Margaria P, Nagata T, Winter S, Blawid R. Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent. Virus Genes 2022; 58:294-307. [PMID: 35538384 DOI: 10.1007/s11262-022-01903-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bulbifera, D. subhastata, and D. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only in D. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled from HTS and one by Sanger sequencing to group the sequences in a clade phylogenetically distinct from YMV from other origins. Temporal phylogenetic analyses estimated the mean evolutionary rate for the CP gene of YMV as 1.76 × 10-3 substitutions per site per year, and the time to the most recent common ancestor as 168.68 years (95% Highest Posterior Density, HPD: 48.56-363.28 years), with a most likely geographic origin in the African continent. The data presented in this study contribute to reveal key aspects of the probable epidemiological history of YMV in Brazil.
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Affiliation(s)
- Alejandro Risco Mendoza
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil. .,Department of Plant Pathology, Agronomy Faculty, Universidad Nacional Agraria La Molina, Lima, Peru.
| | - Paolo Margaria
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Tatsuya Nagata
- Department of Cell Biology, Laboratory of Electron Microscopy and Virology, University of Brasília, Distrito Federal, Brasília, Brazil
| | - Stephan Winter
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Rosana Blawid
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil
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Pielhop TP, Popp C, Knierim D, Margaria P, Maiß E. Three new mycoviruses identified in the apple replant disease (ARD)-associated fungus Rugonectria rugulosa. Virus Genes 2022; 58:423-435. [PMID: 35841525 PMCID: PMC9477930 DOI: 10.1007/s11262-022-01924-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/25/2022] [Indexed: 02/05/2023]
Abstract
In this study, three new mycoviruses were identified co-infecting the apple replant disease (ARD)-associated root endophyte Rugonectria rugulosa. After dsRNA extraction, six viral fragments were visualized. Four fragments belong to a quadrivirus, which has a genome size of 17,166 bp. Each of the fragments of this quadrivirus has a single ORF encoding a protein. Two of these proteins are coat protein subunits, one ORF encodes the RdRp, and one protein has an unknown function. This virus was tentatively named rugonectria rugulosa quadrivirus 1 (RrQV1) as a member of the proposed new species Quadrivirus rugonectria. Another fragment represents the dsRNA intermediate form of a + ssRNA mitovirus with a genome size of 2410 nt. This virus encodes an RdRp and is tentatively called rugonectria rugulosa mitovirus 1 (RrMV1). RrMV1 is suggested as a member of a new species with the proposed name Mitovirus rugonectria. The sixth fragment belongs to the genome of an unclassified dsRNA virus tentatively called rugonectria rugulosa dsRNA virus 1 (RrV1). The monopartite dsRNA genome of RrV1 has a length of 8964 bp and contains two ORFs encoding a structure/gag protein and an RdRp. Full genomic sequences were determined and the genome structure as well as molecular properties are presented. After phylogenetic studies and sequence identity analyses, all three isolates are proposed as new mycoviruses. The results help to improve the understanding of the complexity of the factors involved in ARD and support the interest in mycoviral research. Subsequent analyses need to focus on the impact of mycoviruses on the biology and pathogenicity of ARD-associated fungi. The results of such studies could contribute to the development of mitigation strategies against the disease.
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Affiliation(s)
- Tom P. Pielhop
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Carolin Popp
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Dennis Knierim
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Brunswick, Germany
| | - Paolo Margaria
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Brunswick, Germany
| | - Edgar Maiß
- Institute of Horticultural Production Systems, Department of Phytomedicine, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Lindenau S, Winter S, Margaria P. The Amino-Proximal Region of the Coat Protein of Cucumber Vein Yellowing Virus (Family Potyviridae) Affects the Infection Process and Whitefly Transmission. Plants (Basel) 2021; 10:plants10122771. [PMID: 34961241 PMCID: PMC8706179 DOI: 10.3390/plants10122771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 05/02/2023]
Abstract
Most plant viruses rely on vector transmission for their spread and specific interactions between vector and virus have evolved to regulate this relationship. The whitefly Bemisia tabaci- transmitted cucumber vein yellowing virus (CVYV; genus Ipomovirus, family Potyviridae) is endemic in the Mediterranean Basin, where it causes significant losses in cucurbit crops. In this study, the role of the coat protein (CP) of CVYV for B. tabaci transmission and plant infection was investigated using a cloned and infectious CVYV cDNA and a collection of point and deletion mutants derived from this clone. Whitefly transmission of CVYV was abolished in a deletion mutant lacking amino acids in position 93-105 of the CP. This deletion mutant caused more severe disease symptoms compared to the cDNA clone representing the wild-type (wt) virus and movement efficiency was likewise affected. Two virus mutants carrying a partially restored CP were transmissible and showed symptoms comparable to the wt virus. Collectively, our data demonstrate that the N-terminus of the CVYV CP is a determinant for transmission by the whitefly vector and is involved in plant infection and symptom expression.
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Kutnjak D, Tamisier L, Adams I, Boonham N, Candresse T, Chiumenti M, De Jonghe K, Kreuze JF, Lefebvre M, Silva G, Malapi-Wight M, Margaria P, Mavrič Pleško I, McGreig S, Miozzi L, Remenant B, Reynard JS, Rollin J, Rott M, Schumpp O, Massart S, Haegeman A. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms 2021; 9:841. [PMID: 33920047 PMCID: PMC8071028 DOI: 10.3390/microorganisms9040841] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Lucie Tamisier
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Ian Adams
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Neil Boonham
- Institute for Agri-Food Research and Innovation, Newcastle University, King’s Rd, Newcastle Upon Tyne NE1 7RU, UK;
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council, Via Amendola, 122/D, 70126 Bari, Italy;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
| | - Jan F. Kreuze
- International Potato Center (CIP), Avenida la Molina 1895, La Molina, Lima 15023, Peru;
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK;
| | - Martha Malapi-Wight
- Biotechnology Risk Analysis Programs, Biotechnology Regulatory Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Riverdale, MD 20737, USA;
| | - Paolo Margaria
- Leibniz Institute-DSMZ, Inhoffenstrasse 7b, 38124 Braunschweig, Germany;
| | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia;
| | - Sam McGreig
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy;
| | - Benoit Remenant
- ANSES Plant Health Laboratory, 7 Rue Jean Dixméras, CEDEX 01, 49044 Angers, France;
| | | | - Johan Rollin
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
- DNAVision, 6041 Charleroi, Belgium
| | - Mike Rott
- Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada;
| | - Olivier Schumpp
- Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (J.-S.R.); (O.S.)
| | - Sébastien Massart
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
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Munganyinka E, Margaria P, Sheat S, Ateka EM, Tairo F, Ndunguru J, Winter S. Localization of cassava brown streak virus in Nicotiana rustica and cassava Manihot esculenta (Crantz) using RNAscope® in situ hybridization. Virol J 2018; 15:128. [PMID: 30107851 PMCID: PMC6092782 DOI: 10.1186/s12985-018-1038-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/02/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Cassava brown streak disease (CBSD) has a viral aetiology and is caused by viruses belonging to the genus Ipomovirus (family Potyviridae), Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Molecular and serological methods are available for detection, discrimination and quantification of cassava brown streak viruses (CBSVs) in infected plants. However, precise determination of the viral RNA localization in infected host tissues is still not possible pending appropriate methods. RESULTS We have developed an in situ hybridization (ISH) assay based on RNAscope® technology that allows the sensitive detection and localization of CBSV RNA in plant tissues. The method was initially developed in the experimental host Nicotiana rustica and was then further adapted to cassava. Highly sensitive and specific detection of CBSV RNA was achieved without background and hybridization signals in sections prepared from non-infected tissues. The tissue tropism of CBSV RNAs appeared different between N. rustica and cassava. CONCLUSIONS This study provides a robust method for CBSV detection in the experimental host and in cassava. The protocol will be used to study CBSV tropism in various cassava genotypes, as well as CBSVs/cassava interactions in single and mixed infections.
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Affiliation(s)
- Esperance Munganyinka
- Rwanda Agriculture Board, P.O. Box 5016, Kigali, Rwanda
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Paolo Margaria
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Plant Virus Department, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Samar Sheat
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Plant Virus Department, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Elijah M. Ateka
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Stephan Winter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Plant Virus Department, Messeweg 11/12, 38104 Braunschweig, Germany
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Zhao K, Margaria P, Rosa C. Characterization of the first complete genome sequence of an Impatiens necrotic spot orthotospovirus isolate from the United States and worldwide phylogenetic analyses of INSV isolates. BMC Res Notes 2018; 11:288. [PMID: 29747679 PMCID: PMC5946465 DOI: 10.1186/s13104-018-3395-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/03/2018] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE Impatiens necrotic spot orthotospovirus (INSV) can impact economically important ornamental plants and vegetables worldwide. Characterization studies on INSV are limited. For most INSV isolates, there are no complete genome sequences available. This lack of genomic information has a negative impact on the understanding of the INSV genetic diversity and evolution. Here we report the first complete nucleotide sequence of a US INSV isolate. RESULTS INSV-UP01 was isolated from an impatiens in Pennsylvania, US. RT-PCR was used to clone its full-length genome and Vector NTI to assemble overlapping sequences. Phylogenetic trees were constructed by using MEGA7 software to show the phylogenetic relationships with other available INSV sequences worldwide. This US isolate has genome and biological features classical of INSV species and clusters in the Western Hemisphere clade, but its origin appears to be recent. Furthermore, INSV-UP01 might have been involved in a recombination event with an Italian isolate belonging to the Asian clade. Our analyses support that INSV isolates infect a broad plant-host range they group by geographic origin and not by host, and are subjected to frequent recombination events. These results justify the need to generate and analyze complete genome sequences of orthotospoviruses in general and INSV in particular.
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Affiliation(s)
- Kaixi Zhao
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802 USA
| | - Paolo Margaria
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802 USA
- Plant Virus Department, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Brunswick, Germany
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802 USA
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Bertran A, Ciuffo M, Margaria P, Rosa C, Oliveira Resende R, Turina M. Host-specific accumulation and temperature effects on the generation of dimeric viral RNA species derived from the S-RNA of members of the Tospovirus genus. J Gen Virol 2016; 97:3051-3062. [PMID: 27600541 DOI: 10.1099/jgv.0.000598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Polygonum ringspot virus (PolRSV) is a recently characterized Tospovirus reported in Italy. Northern blot analyses of PolRSV infections in Nicotiana benthamiana and tomato plants showed that a viral RNA species with nearly twice the length of the Small genomic RNA (S-RNA) accumulated abundantly in the former host, but was not detected in the latter. Additional assays confirmed that biogenesis of this novel RNA species was common to all PolRSV isolates tested and also to an isolate of Tomato spotted wilt virus (TSWV). Given its size, we hypothesized that the novel RNA species was a dimer molecule and we confirmed this hypothesis by RNA sequencing (RNAseq) analysis and reverse transcription (RT)-PCR of putative predicted dimer junction sites in RNA extracts of N. benthamiana challenged with PolRSV isolates Plg6 and Plg13/2. We also confirmed that these molecules are derived from head-to-tail dimers and often contain deletions at their junction sites. We named these novel molecules imperfect dimer RNAs (IMPD-RNAs). PolRSV IMPD-RNAs systemic accumulation in a range of host plants was restricted to N. benthamiana and Nicotiana occidentalis. Notably, IMPD-RNAs accumulation was modulated by temperature and their generation was restricted to late stages of systemic infection (12 days post-inoculation) in N. benthamiana. Differently from all other PolRSV isolates used in this study, Plg13/2 generated more IMPD-RNAs coupled with low amounts of genomic S-RNA and maintained them even at 18 °C, besides having lost the ability to infect tomato plants. This is the first characterization of S-RNA dimers for Tospovirus, and of occurrence of dimers of genomic segments at the whole organism level for Bunyaviridae.
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Affiliation(s)
- André Bertran
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
- Plant Virology Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
| | - Paolo Margaria
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Renato Oliveira Resende
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
- Plant Virology Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
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Margaria P, Anderson CT, Turina M, Rosa C. Identification of Ourmiavirus 30K movement protein amino acid residues involved in symptomatology, viral movement, subcellular localization and tubule formation. Mol Plant Pathol 2016; 17:1063-79. [PMID: 26637973 PMCID: PMC6638536 DOI: 10.1111/mpp.12348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/26/2015] [Indexed: 05/03/2023]
Abstract
Several plant viruses encode movement proteins (MPs) classified in the 30K superfamily. Despite a great functional diversity, alignment analysis of MP sequences belonging to the 30K superfamily revealed the presence of a central core region, including amino acids potentially critical for MP structure and functionality. We performed alanine-scanning mutagenesis of the Ourmia melon virus (OuMV) MP, and studied the effects of amino acid substitutions on MP properties and virus infection. We identified five OuMV mutants that were impaired in systemic infection in Nicotiana benthamiana and Arabidopsis thaliana, and two mutants showing necrosis and pronounced mosaic symptoms, respectively, in N. benthamiana. Green fluorescent protein fusion constructs (GFP:MP) of movement-defective MP alleles failed to localize in distinct foci at the cell wall, whereas a GFP fusion with wild-type MP (GFP:MPwt) mainly co-localized with plasmodesmata and accumulated at the periphery of epidermal cells. The movement-defective mutants also failed to produce tubular protrusions in protoplasts isolated from infected leaves, suggesting a link between tubule formation and the ability of OuMV to move. In addition to providing data to support the importance of specific amino acids for OuMV MP functionality, we predict that these conserved residues might be critical for the correct folding and/or function of the MP of other viral species in the 30K superfamily.
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Affiliation(s)
- Paolo Margaria
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Charles T Anderson
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, 10135, Torino, Italy
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, 16802, USA
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Margaria P, Miozzi L, Ciuffo M, Rosa C, Axtell MJ, Pappu HR, Turina M. Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection. Virus Res 2016; 211:38-45. [PMID: 26432447 DOI: 10.1016/j.virusres.2015.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/22/2015] [Accepted: 09/25/2015] [Indexed: 11/19/2022]
Abstract
Viral small RNAs (vsRNAs) are one of the key elements involved in RNA silencing-based defense against viruses in plants. We analyzed the vsRNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot virus (PolRSV) (Tospovirus, Bunyaviridae). VsRNAs were abundant in both hosts, but a different size profile was observed, with an abundance peak at 21 in N. benthamiana and at 22 nt in tomato. VsRNAs mapping to the PolRSV L genomic segment were under-represented in both hosts, while S and M segments were differentially and highly targeted in N. benthamiana and tomato, respectively. Differences in preferential targeting of single ORFs were observed, with over-representation of NSs ORF-derived reads in N. benthamiana. Intergenic regions (IGRs)-mapping vsRNAs were under-represented, while enrichment of vsRNAs reads mapping to the NSs positive sense strand was observed in both hosts. Comparison with a previous study on tomato spotted wilt virus (TSWV) under the same experimental conditions, showed that the relative accumulation of PolRSV-specific and endogenous sRNAs was similar to the one observed for silencing suppressor-deficient TSWV strains, suggesting possible different properties of PolRSV NSs silencing suppressor compared to that of TSWV.
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Affiliation(s)
- Paolo Margaria
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Miozzi
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Marina Ciuffo
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, WA 99164, USA
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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Margaria P, Miozzi L, Rosa C, Axtell MJ, Pappu HR, Turina M. Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana. Virus Res 2015; 208:30-8. [PMID: 26047586 DOI: 10.1016/j.virusres.2015.05.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/25/2015] [Accepted: 05/25/2015] [Indexed: 01/01/2023]
Abstract
Tospoviruses are plant-infecting viruses belonging to the family Bunyaviridae. We used a collection of wild-type, phylogenetically distinct tomato spotted wilt virus isolates and related silencing-suppressor defective mutants to study the effects on the small RNA (sRNA) accumulation during infection of Nicotiana benthamiana. Our data showed that absence of a functional silencing suppressor determined a marked increase of the total amount of viral sRNAs (vsRNAs), and specifically of the 21 nt class. We observed a common under-representation of vsRNAs mapping to the intergenic region of S and M genomic segments, and preferential mapping of the reads against the viral sense open reading frames, with the exception of the NSs gene. The NSs-mutant strains showed enrichment of NSm-derived vsRNA compared to the expected amount based on gene size. Analysis of 5' terminal nucleotide preference evidenced a significant enrichment in U for the 21 nt- and in A for 24 nt-long endogenous sRNAs in all the samples. Hotspot analysis revealed a common abundant accumulation of reads at the 5' end of the L segment, mostly in the antiviral sense, for the NSs-defective isolates, suggesting that absence of the silencing suppressor can influence preferential targeting of the viral genome.
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Affiliation(s)
- Paolo Margaria
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Miozzi
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, WA 99164, USA
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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Margaria P, Rosa C. First complete genome sequence of a tomato spotted wilt virus isolate from the United States and its relationship to other TSWV isolates of different geographic origin. Arch Virol 2015; 160:2915-20. [PMID: 26329831 DOI: 10.1007/s00705-015-2589-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/26/2015] [Indexed: 01/13/2023]
Abstract
We report the first complete nucleotide sequence of a tomato spotted wilt virus (genus Tospovirus, family Bunyaviridae) isolate from the United States. The tripartite genome of PA01 consisted of L, M and S RNAs of 8914, 4765 and 2984 nt, respectively. Similarity percentages in nucleotide and amino acid sequence among PA01 and previously characterized TSWV isolates are provided here. Phylogenetic analysis on the RNA-dependent RNA polymerase (RdRp) gene placed PA01 in a different clade from an isolate from Hawaii that was partially characterized previously. Evidence of two putative reassortment events in the M segment, among PA01 and isolates from South Korea, Italy and Brazil, was found by phylogenetic and recombination analysis, further supporting a role for genetic exchange among isolates of different geographic origin in TSWV evolution.
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Affiliation(s)
- Paolo Margaria
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
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Margaria P, Ciuffo M, Rosa C, Turina M. Evidence of a tomato spotted wilt virus resistance-breaking strain originated through natural reassortment between two evolutionary-distinct isolates. Virus Res 2015; 196:157-61. [DOI: 10.1016/j.virusres.2014.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 02/03/2023]
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Margaria P, Ferrandino A, Caciagli P, Kedrina O, Schubert A, Palmano S. Metabolic and transcript analysis of the flavonoid pathway in diseased and recovered Nebbiolo and Barbera grapevines (Vitis vinifera L.) following infection by Flavescence dorée phytoplasma. Plant Cell Environ 2014; 37:2183-200. [PMID: 24689527 DOI: 10.1111/pce.12332] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 05/05/2023]
Abstract
Flavescence dorée phytoplasma (FDp) infections seriously affect production and survival of grapevine. We analysed the changes in the flavonoid pathway occurring in two red cultivars, the highly susceptible Barbera and the less susceptible Nebbiolo, following FDp infection. A combination of metabolic and transcript analyses was used to quantify flavonoid compounds and expression of a set of genes involved in their biosynthesis. Quantification of anthocyanins, flavonols, proanthocyanidins and related biosynthetic enzymes was performed over the vegetative season, at four time points, on healthy, infected and recovered plants. A strong activation of anthocyanin accumulation was observed in infected Barbera leaves, while the response was less marked in Nebbiolo. Proanthocyanidins also accumulated mainly in infected Barbera leaves, even if basal proanthocyanidin concentration was higher in healthy and recovered Nebbiolo. Biochemical data were supported by transcript analysis: genes of the stem flavonoid pathway and of the anthocyanin and proanthocyanidin branches were expressed at a higher level in infected than in healthy plants, with a different magnitude between the two cultivars. Based on our results, we hypothesize that flavonoid accumulation is a physiological consequence of FD infection without affecting phytoplasma multiplication, although proanthocyanidin accumulation could help repel further infection by the insect vector.
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Affiliation(s)
- Paolo Margaria
- Istituto di Virologia Vegetale, CNR, 10135, Torino, Italy
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Margaria P, Miozzi L, Ciuffo M, Pappu H, Turina M. The complete genome sequence of polygonum ringspot virus. Arch Virol 2014; 159:3149-52. [PMID: 25000901 DOI: 10.1007/s00705-014-2166-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
Abstract
The complete genome sequence of polygonum ringspot virus (PolRSV), genus Tospovirus, family Bunyaviridae, was determined. This is the first report of the complete genome sequence for a European tospovirus isolate. The large RNA of PolRSV was 8893 nucleotides (nt) in size and contained a single open reading frame of 8628 nucleotides in the viral-complementary sense, coding for a predicted RNA-dependent RNA polymerase of 330.9 kDa. Two untranslated regions of 230 and 32 nucleotides were present at the 5' and 3' termini, respectively, which showed conserved terminal sequences, as commonly observed for tospovirus genomic RNAs. The medium and small (S) RNAs were 4710 and 2485 nucleotides in size, respectively, and showed 99 % homology to the corresponding genomic segment of a previously partially characterized PolRSV isolate, Plg3. Protein sequences for GN/GC, N and NSs were identical in length in the two PolRSV isolates, while an amino acid insertion was observed for the NSm protein of the newly characterized isolate. The noncoding intergenic region of the S RNA was very short (183 nt) and was not predicted to form a hairpin structure, confirming that this unique characteristic within tospoviruses, previously observed for Plg3, is not isolate specific.
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Affiliation(s)
- P Margaria
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Strada delle Cacce 73, 10135, Turin, Italy
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Margaria P, Bosco L, Vallino M, Ciuffo M, Mautino GC, Tavella L, Turina M. The NSs protein of tomato spotted wilt virus is required for persistent infection and transmission by Frankliniella occidentalis. J Virol 2014; 88:5788-802. [PMID: 24623427 PMCID: PMC4019118 DOI: 10.1128/jvi.00079-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/04/2014] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Tomato spotted wilt virus (TSWV) is the type member of tospoviruses (genus Tospovirus), plant-infecting viruses that cause severe damage to ornamental and vegetable crops. Tospoviruses are transmitted by thrips in the circulative propagative mode. We generated a collection of NSs-defective TSWV isolates and showed that TSWV coding for truncated NSs protein could not be transmitted by Frankliniella occidentalis. Quantitative reverse transcription (RT)-PCR and immunostaining of individual insects detected the mutant virus in second-instar larvae and adult insects, demonstrating that insects could acquire and accumulate the NSs-defective virus. Nevertheless, adults carried a significantly lower viral load, resulting in the absence of transmission. Genome sequencing and analyses of reassortant isolates showed genetic evidence of the association between the loss of competence in transmission and the mutation in the NSs coding sequence. Our findings offer new insight into the TSWV-thrips interaction and Tospovirus pathogenesis and highlight, for the first time in the Bunyaviridae family, a major role for the S segment, and specifically for the NSs protein, in virulence and efficient infection in insect vector individuals. IMPORTANCE Our work is the first to show a role for the NSs protein in virus accumulation in the insect vector in the Bunyaviridae family: demonstration was obtained for the system TSWV-F. occidentalis, arguably one of the most damaging combination for vegetable crops. Genetic evidence of the involvement of the NSs protein in vector transmission was provided with multiple approaches.
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Affiliation(s)
- P. Margaria
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Turin, Italy
| | - L. Bosco
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Turin, Grugliasco (TO), Italy
| | - M. Vallino
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Turin, Italy
| | - M. Ciuffo
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Turin, Italy
| | - G. C. Mautino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Turin, Grugliasco (TO), Italy
| | - L. Tavella
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Turin, Grugliasco (TO), Italy
| | - M. Turina
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Turin, Italy
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Ciuffo M, Pacifico D, Margaria P, Turina M. A new ilarvirus isolated from Viola × wittrockiana and its detection in pansy germoplasm by qRT-PCR. Arch Virol 2014; 159:561-5. [PMID: 24048886 DOI: 10.1007/s00705-013-1837-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
Abstract
An infectious agent was transmitted mechanically from samples of Viola spp. showing white mosaic and leaf deformation to Nicotiana benthamiana. dsRNA extracted from the N. benthamiana plants migrated as four specific bands that were absent in non-inoculated plants. Sequence analysis of cDNA clones generated from the second-smallest dsRNA showed the greatest similarity to the RNA3 of prune dwarf virus (PDV) (genus Ilarvirus, family Bromoviridae). However, because of differences in molecular, biological, and serological properties between this virus isolate and PDV, a new ilarvirus species, named "Viola white distortion associated virus" (VWDaV) is proposed. Specific oligonucleotides and a TaqMan(®) probe were designed for diagnostic purposes. The possible association between the virus and the original white distortion symptoms is discussed.
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Affiliation(s)
- M Ciuffo
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Strada delle Cacce n73, 10135, Turin, Italy
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Gambino G, Boccacci P, Margaria P, Palmano S, Gribaudo I. Hydrogen peroxide accumulation and transcriptional changes in grapevines recovered from flavescence dorée disease. Phytopathology 2013; 103:776-84. [PMID: 23489524 DOI: 10.1094/phyto-11-12-0309-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Flavescence dorée (FD) is considered one of the most severe phytoplasma diseases affecting grapevine. The spontaneous, complete, and stable remission of the symptoms of FD (recovery) is a phenomenon that may occur in infected grapevines. The molecular bases of this phenomenon are still unclear, although some works suggest that recovery could be linked to the accumulation of hydrogen peroxide (H2O2). Several genes coding for enzymes involved in H2O2 metabolism, in the ascorbate-glutathione cycle, defense responses, and the biosynthesis of hormones were identified. The H2O2 content was biochemically determined and the expression levels of 44 genes were analyzed through quantitative real-time reverse-transcription polymerase chain reaction in healthy (H), infected by FD-associated phytoplasma (I), and 2-years-recovered (R) plants of Vitis vinifera 'Barbera'. In tissues of R plants, large amounts of H2O2 were detected, essentially linked to an upregulation of genes involved in the production of H2O2 (germin-like protein and glycolate oxidase); whereas, in I grapevines, the overexpression of some scavenging genes reduced the quantity of H2O2. The recovery state was characterized by the activation of ethylene biosynthesis and of defense genes not linked to salicylic acid (SA) signaling, such as the WRKY2 transcription factor. Conversely, I plants reacted to phytoplasma with SA-mediated signaling, even though this response does not appear to be effective against the pathogen.
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Margaria P, Abbà S, Palmano S. Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks. BMC Genomics 2013; 14:38. [PMID: 23327683 PMCID: PMC3564869 DOI: 10.1186/1471-2164-14-38] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 01/09/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, localization and interaction with other partners. In this work, we used a multiplex staining approach with 2D gels to study quantitative changes in the proteome and phosphoproteome of Flavescence dorée-affected and recovered 'Barbera' grapevines, compared to healthy plants. RESULTS We identified 48 proteins that differentially changed in abundance, phosphorylation, or both in response to Flavescence dorée phytoplasma infection. Most of them did not show any significant difference in recovered plants, which, by contrast, were characterized by changes in abundance, phosphorylation, or both for 17 proteins not detected in infected plants. Some enzymes involved in the antioxidant response that were up-regulated in infected plants, such as isocitrate dehydrogenase and glutathione S-transferase, returned to healthy-state levels in recovered plants. Others belonging to the same functional category were even down-regulated in recovered plants (oxidoreductase GLYR1 and ascorbate peroxidase). Our proteomic approach thus agreed with previously published biochemical and RT-qPCR data which reported down-regulation of scavenging enzymes and accumulation of H2O2 in recovered plants, possibly suggesting a role for this molecule in remission from infection. Fifteen differentially phosphorylated proteins (| ratio | > 2, p < 0.05) were identified in infected compared to healthy plants, including proteins involved in photosynthesis, response to stress and the antioxidant system. Many were not differentially phosphorylated in recovered compared to healthy plants, pointing to their specific role in responding to infection, followed by a return to a steady-state phosphorylation level after remission of symptoms. Gene ontology (GO) enrichment and statistical analysis showed that the general main category "response to stimulus" was over-represented in both infected and recovered plants but, in the latter, the specific child category "response to biotic stimulus" was no longer found, suggesting a return to steady-state levels for those proteins specifically required for defence against pathogens. CONCLUSIONS Proteomic data were integrated into biological networks and their interactions were represented through a hypothetical model, showing the effects of protein modulation on primary metabolic ways and related secondary pathways. By following a multiplex-staining approach, we obtained new data on grapevine proteome pathways that specifically change at the phosphorylation level during phytoplasma infection and following recovery, focusing for the first time on phosphoproteome changes during pathogen infection in this host.
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Affiliation(s)
- Paolo Margaria
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - Simona Abbà
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - Sabrina Palmano
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
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Margaria P, Palmano S. Reverse transcription-PCR for phytoplasma detection utilizing crude sap extractions. Methods Mol Biol 2013; 938:283-289. [PMID: 22987424 DOI: 10.1007/978-1-62703-089-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phytoplasmas are routinely detected by nucleic acid-based techniques. These approaches rely on enriched phytoplasma DNA extracts of good quality, following labor intensive and time-consuming purification protocols. Here we describe a very rapid, specific, sensitive, and reliable method for flavescence dorée phytoplasma detection, based on real-time Taqman(®) reverse transcription-PCR of the 16S rRNA. The protocol is particularly useful for large-scale screening of vineyards and nurseries, pathogen surveys, and field epidemiological studies.
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Zindović J, Bulajić A, Krstić B, Ciuffo M, Margaria P, Turina M. First Report of Tomato spotted wilt virus on Pepper in Montenegro. Plant Dis 2011; 95:882. [PMID: 30731705 DOI: 10.1094/pdis-03-11-0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In April 2009, chlorotic and necrotic ring spots, chlorotic line patterns, and stunting were observed on greenhouse-grown pepper plants in the vicinity of Podgorica, Montenegro. Disease symptom incidence was estimated at 40%. Symptomatic leaves were tested for the presence of Tomato spotted wilt virus (TSWV) with a commercial double-antibody sandwich (DAS)-ELISA diagnostic kit (Bioreba AG, Reinach, Switzerland). Commercial positive and negative controls were included in each ELISA. TSWV was detected serologically in 33 of 75 pepper samples. The virus was mechanically transmitted from ELISA-positive pepper samples to Nicotiana tabacum cv. Samsun using chilled 0.05 M phosphate buffer (pH 7) containing 0.1% sodium sulfite (1). Inoculated test plants produced chlorotic and necrotic concentric rings and necrotic spots, consistent with symptoms caused by TSWV on N. tabacum. For further confirmation of TSWV infection, reverse transcription (RT)-PCR was performed with the One-Step RT-PCR Kit (Qiagen, Hilden, Germany) using three sets of primers: S70-for/S890-rev (2) and S574-for/S1433-rev (3), both specific to the nonstructural (NSs) gene; and S1983-for/S2767-rev (2), specific to the nucleocapsid protein (N) gene. Total RNAs from naturally infected pepper and symptomatic N. tabacum cv. Samsun plants were extracted with the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Total RNAs obtained from the Italian isolate of TSWV (GenBank Accession No. DQ398945) and healthy tobacco plants were used as positive and negative controls, respectively. The expected sizes of the RT-PCR products (820, 859, and 784 bp) were amplified from symptomatic pepper samples but not from healthy tissues. The PCR product obtained from isolate Is-344 using primers specific to N gene was purified by a QIAquick PCR Purification Kit (Qiagen), cloned into the pGEM-T Easy Vector (Promega, Madison, WI) and sequenced in both directions using the same primer pair as in RT-PCR. The sequences amplified with the two primer pairs specific to the NSs gene were obtained by direct sequencing (Bio-Fab Research Srl, Pomezia, Italy) and joined using MEGA4 software. Sequence analysis of the complete N gene (777 bp; GenBank Accession No. GU369717) revealed that the TSWV isolate originating from Montenegro shared 98.2 to 99.7% nucleotide identity (98.1 to 100% amino acid identities) with corresponding TSWV sequences deposited in GenBank. The Montenegrin isolate Is-344 was most closely related to Italian isolates from tomato (GU369725) and eggplant (GU369720). The partial (1,257 bp) nucleotide sequence of NSs gene (GU369737) showed 96 to 99.8% nucleotide identity (96.9 to 100% amino acid identity) with previously reported TSWV sequences, and in this case the highest identity was with French isolates from tomato (FR692835) and lettuce (FR692831). To our knowledge, this is the first report on the occurrence of TSWV in Montenegro. Data of this study sheds light on the importance of further survey studies and inspections of TSWV-susceptible crops cultivated in Montenegro. References: (1) Anonymous. OEPP/EPPO Bull. 29:465, 1999. (2) W. P. Qiu et al. Virology 244:186, 1998. (3) M. Tsompana et al. Mol. Ecol. 14:53, 2005.
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Affiliation(s)
- J Zindović
- Department of Plant Protection, University of Montenegro-Biotechnical Faculty, Mihajla Lalića 1, 81000 Podgorica, Montenegro
| | - A Bulajić
- Institute of Plant Protection, Department of Phytopathology, University of Belgrade-Faculty of Agriculture, Nemanjina 6, 11080 Belgrade, Serbia
| | - B Krstić
- Institute of Plant Protection, Department of Phytopathology, University of Belgrade-Faculty of Agriculture, Nemanjina 6, 11080 Belgrade, Serbia
| | - M Ciuffo
- Institute for Plant Virology, National Research Council, Strada delle Cacce 73, 10135 Turin, Italy
| | - P Margaria
- Institute for Plant Virology, National Research Council, Strada delle Cacce 73, 10135 Turin, Italy
| | - M Turina
- Institute for Plant Virology, National Research Council, Strada delle Cacce 73, 10135 Turin, Italy
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Margaria P, Palmano S. Response of the Vitis vinifera L. cv. 'Nebbiolo' proteome to Flavescence dorée phytoplasma infection. Proteomics 2010; 11:212-24. [PMID: 21204249 DOI: 10.1002/pmic.201000409] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 10/11/2010] [Accepted: 10/18/2010] [Indexed: 01/05/2023]
Abstract
Flavescence dorée is a serious phytoplasma disease affecting grapevine in several European countries. We studied the interaction of Flavescence dorée phytoplasma with its natural plant host by monitoring the effects of infection on the protein expression profile. Among the 576 analyzed spots, 33 proteins were differentially regulated in infected grapevines. Grouping into MIPS functional categories showed proteins involved in metabolism (21%), energy processes (9%), protein synthesis (3%), protein fate (18%), cellular transport and transport routes (6%), cell defense and virulence (42%). Among the differentially regulated proteins, we selected six targets (thaumatin I, thaumatin II, osmotin-like protein, plant basic secretory protein, AAA(+) Rubisco activase and proteasome α5 subunit) and we analyzed their expression by quantitative RT-PCR on samples collected in 2008 and 2009 in several vineyards in Piedmont region, Italy. There was a positive correlation between mRNA and protein expression for most of the genes in both the years. We discuss the involvement of these proteins in the specific response to phytoplasma infection. To our knowledge, this work is the first to investigate the response of the grapevine proteome to Flavescence dorée phytoplasma infection, and provides reference protein profiles for future comparative proteomic and genomic studies.
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Margaria P, Rosa C, Marzachì C, Turina M, Palmano S. Detection of Flavescence Dorée Phytoplasma in Grapevine by Reverse-Transcription PCR. Plant Dis 2007; 91:1496-1501. [PMID: 30780745 DOI: 10.1094/pdis-91-11-1496] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavescence dorée (FD) is the most serious phytoplasma disease of grapevine. This report describes a novel method of detecting FD phytoplasma based on reverse-transcription polymerase chain reaction (RT-PCR) on 16S ribosomal RNA (16SrRNA) which will greatly improve mass screening of infected grapevines. A rapid protocol for extracting sap from whole leaves or midveins and successive one-tube amplification by RT-PCR was applied to grapevine samples with or without symptoms collected from different areas of Piedmont (northwestern Italy). Results were compared with those obtained using one of the current diagnostic methods that utilizes nested PCR on phytoplasma DNA-enriched preparations. A Cohen's kappa index of 0.76 indicated a substantial agreement between the two sets of results. The RT-PCR method has the advantage of being a rapid, reliable, and sensitive assay for large-scale screening of grapevines.
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Affiliation(s)
- P Margaria
- Istituto di Virologia Vegetale, CNR, 10135 Torino, Italy
| | - C Rosa
- University of California, Department of Plant Pathology, Davis 95616
| | - C Marzachì
- Istituto di Virologia Vegetale, CNR, Torino
| | - M Turina
- Istituto di Virologia Vegetale, CNR, Torino
| | - S Palmano
- Istituto di Virologia Vegetale, CNR, Torino
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Margaria P, Ciuffo M, Pacifico D, Turina M. Evidence that the nonstructural protein of Tomato spotted wilt virus is the avirulence determinant in the interaction with resistant pepper carrying the TSW gene. Mol Plant Microbe Interact 2007; 20:547-58. [PMID: 17506332 DOI: 10.1094/mpmi-20-5-0547] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
All known pepper cultivars resistant to Tomato spotted wilt virus (TSWV) possess a single dominant resistance gene, Tsw. Recently, naturally occurring resistance-breaking (RB) TSWV strains have been identified, causing major concerns. We used a collection of such strains to identify the specific genetic determinant that allows the virus to overcome the Tsw gene in Capsicum spp. A reverse genetic approach is still not feasible for TSWV; therefore, we analyzed reassortants between wild-type (WT) and RB strains. Our results confirmed that the S RNA, which encodes both the nucleocapsid protein (N) and a nonstructural protein (NSs), carries the genetic determinant responsible for Tsw resistance breakdown. We then used full-length S RNA segments or the proteins they encode to compare the sequences of WT and related RB strains, and obtained indirect evidence that the NSs protein is the avirulence factor in question. Transient expression of NSs protein from WT and RB strains showed that they both can equally suppress post-transcriptional gene silencing (PTGS). Moreover, biological characterization of two RB strains carrying deletions in the NSs protein showed that NSs is important in maintaining TSWV infection in newly emerging leaves over time, preventing recovery. Analysis of another RB strain phenotype allowed us to conclude that local necrotic response is not sufficient for resistance in Capsicum spp. carrying the Tsw gene.
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Affiliation(s)
- P Margaria
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Strada delle Cacce 73, Torino 10135, Italy
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