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Wang R, Liu S, Xu C, Yu J, Wei J, Ding W, Li Y. Identification and characterization of a novel Cytorhabdovirus associated with goji berry ( Lycium barbarum L.) crinkle disease. Front Microbiol 2024; 14:1294616. [PMID: 38239727 PMCID: PMC10794335 DOI: 10.3389/fmicb.2023.1294616] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Goji berry (Lycium barbarum L.) is a traditional Chinese herbal medicinal plant that is extensively cultivated in the arid and semiarid regions of northwest China. In this study, a novel cytorhabdovirus, tentatively named "goji cytorhabdovirus A (GCVA)," was identified from the goji berry plant exhibiting leaf crinkle symptoms through high-throughput sequencing (HTS). GCVA contains a linear, negative sense single-stranded RNA genome of 14,812 nucleotides and encodes six open reading frames in the order of 3' leader-N-P-P4-M-G-L-5' trailer. The genome of GCVA shares the highest nucleotide (nt) identity of 65.80% (16% query coverage) with yerba mate virus A (YmVA) (NC_076472). The N and L proteins also share low amino acid (aa) identities (<35.42 and < 41.23%, respectively) with known cytorhabdoviruses. Typical features of the viruses in the genus Cytorhabdovirus include a highly conserved consensus sequence in the intergenic regions and extensive complementation of the 5' non-coding trailer and the 3' leader. These features were also found in GCVA. These data in combination with a phylogenetic analysis that was based on the aa sequences of the N and L proteins support the proposal that GCVA is a new species in the genus Cytorhabdovirus.
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Affiliation(s)
| | | | | | | | | | - Wanlong Ding
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Abrahamian P, Mollov D, Hammond RW, Rivera Y. Coding-complete genome sequence of an isolate of papaya virus E in tomato. Microbiol Resour Announc 2023; 12:e0034423. [PMID: 37594282 PMCID: PMC10508159 DOI: 10.1128/mra.00344-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 08/19/2023] Open
Abstract
An isolate of papaya virus E was identified in tomato fruits from Mexico. The coding-complete genome sequence was determined using high-throughput sequencing. The coding-complete genome is 13,412 nucleotides and contains 8 open reading frames.
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Affiliation(s)
- Peter Abrahamian
- US Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostic Laboratory, Laurel, Maryland, USA
| | - Dimitre Mollov
- US Department of Agriculture, Agriculture Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Rosemarie W. Hammond
- US Department of Agriculture, Agriculture Research Service, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
| | - Yazmin Rivera
- US Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostic Laboratory, Laurel, Maryland, USA
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Orfanidou CG, Beta C, Reynard JS, Tsiolakis G, Katis NI, Maliogka VI. Identification, molecular characterization and prevalence of a novel cytorhabdovirus infecting zucchini crops in Greece. Virus Res 2020; 287:198095. [PMID: 32735997 DOI: 10.1016/j.virusres.2020.198095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/02/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 02/08/2023]
Abstract
A new cytorhabdovirus was identified in zucchini (Cucurbita pepo) in Greece with the aid of high-throughput sequencing technology. The negative-sense, single-stranded genomic RNA of the new virus was determined and includes seven open reading frames in the order 3'-N-P-P3-P4-M-G-L-5' in the antigenomic orientation. Typical rhabdovirus-like particles were observed in infected leaf material. Comparative sequence analysis and phylogenetic reconstructions suggested that the described virus is a new member of the genus Cytorhabdovirus, and it was tentatively named cucurbit cytorhabdovirus 1 (CuCV1). To our knowledge CuCV1 is the first cytorhabdovirus infecting cucurbits in nature. Our surveys indicated that it occurs in a percentage of 36.7 % in zucchini crops in Greece.
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Affiliation(s)
- C G Orfanidou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - C Beta
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - J-S Reynard
- Laboratory of Virology, Agroscope, Route de Duillier 50, 1260, Nyon, Switzerland
| | - G Tsiolakis
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - N I Katis
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - V I Maliogka
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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Yang X, Chen B, Zhang T, Li Z, Xu C, Zhou G. Geographic Distribution and Genetic Diversity of Rice Stripe Mosaic Virus in Southern China. Front Microbiol 2018; 9:3068. [PMID: 30619153 PMCID: PMC6295562 DOI: 10.3389/fmicb.2018.03068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 10/25/2018] [Accepted: 11/28/2018] [Indexed: 01/21/2023] Open
Abstract
Rice stripe mosaic virus (RSMV) transmitted by the leafhopper Recilia dorsalis is a tentative new species in the genus Cytorhabdovirus identified recently in South China. To explore its geographic distribution and genetic diversity, field investigation and viral whole-genome sequencing were conducted in this study. The results indicated that RSMV was present in the rice samples collected across southern China. Twelve representative samples from different geographical regions were selected for viral whole-genome sequencing and the viral genome variation was analyzed in combination with a previously reported RSMV isolate. Identity analysis showed that the genome sequences of 13 RSMV isolates were highly conserved with nucleotide identities over 99.4%. There was a strong negative selection pressure during the evolution of RSMV with more transitions (72.08%) than transversions (27.92%) found between the RSMV isolates. Among the seven genes encoded by RSMV, the P gene was the most variable, followed by N, M, L, and G; the P3 and P6 amino acid sequences were not found to be mutated and no mutations were found in the non-coding region. A phylogenetic tree based on the RSMV whole-genome nucleotide sequences revealed that all RSMV isolates clustered in two groups based on geographical origin. Notably, the L proteins of the Guangxi and Hainan isolates had five and one specific amino acid sites, respectively, suggesting that the L gene has undergone environmental adaptive variation during the dispersal of RSMV.
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Affiliation(s)
- Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhanbiao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Chenhui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
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Samarfard S, Bejerman NE, Dietzgen RG. Distribution and genetic variability of alfalfa dwarf virus, a cytorhabdovirus associated with alfalfa dwarf disease in Argentina. Virus Genes 2018; 54:612-5. [PMID: 29730762 DOI: 10.1007/s11262-018-1563-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
In 2010, a novel cytorhabdovirus named alfalfa dwarf virus (ADV) was detected for the first time in lucerne crops in Argentina showing dwarfism, in mixed infections with several other viruses. ADV appears to be endemic to Argentina and has not been reported elsewhere. In this study, we have investigated the genetic variability of ADV based on the complete nucleoprotein (N) gene of 13 isolates from different lucerne-growing regions in Argentina. Phylogenetic and sequence identity analyses showed that all ADV isolates are closely related and have not diverged more than 1% in the N gene despite geographical separation. These data provide further evidence that ADV is new to science and emerged and spread very recently. A total of 43 single-nucleotide polymorphisms were identified between the ADV isolates studied. Analysis of N gene ORF sequence revealed a mutational bias, with more transitions than transversions. In all cases, the ratio of non-synonymous/synonymous nucleotide changes was < 1, indicating that ADV N gene is under predominantly purifying selection.
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Mann KS, Dietzgen RG. Functional analysis of a weak viral RNA silencing suppressor using two GFP variants as silencing inducers. J Virol Methods 2017; 239:50-57. [PMID: 27836657 DOI: 10.1016/j.jviromet.2016.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 06/09/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 11/24/2022]
Abstract
RNA silencing in plants can be triggered by the introduction of an exogenous gene. Green fluorescent protein (GFP) has been widely used as a visual reporter to study RNA silencing and viral-mediated suppression of RNA silencing in the model plant Nicotiana benthamiana. In transgenic N. benthamiana plants expressing an endoplasmic reticulum targeted GFP variant (16c) known as mGFP5, RNA silencing can be induced by ectopic over-expression of mGFP5. However, other GFP variants can also be used to induce GFP silencing in these plants. We compared the efficiency to induce local and systemic silencing of two commonly used GFP variants: enhanced GFP (eGFP) and mGFP5. Using lettuce necrotic yellows virus (LNYV) P protein to suppress GFP silencing, we demonstrate that eGFP gene, which is 76% identical at the nucleotide level to the endogenously expressed mGFP5 in 16c plants, triggers silencing more slowly and concurrently prolongs detectable silencing suppressor activity of the weak LNYV P suppressor, compared to the homologous mGFP5 gene. The use of eGFP as RNA silencing inducer in wild type or 16c plants appears to be a useful tool in identifying and analysing weak viral RNA silencing suppressor proteins whose activity might otherwise have been masked when challenged by a stronger RNA silencing response. We also show that reducing the dosage of strong dsRNA silencing inducers in conjunction with their homologous GFP targets facilitates the discovery and analysis of "weaker" RNA silencing suppressor activities.
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Affiliation(s)
- Krin S Mann
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Bejerman N, Giolitti F, de Breuil S, Trucco V, Nome C, Lenardon S, Dietzgen RG. Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses. Virology 2015; 483:275-83. [PMID: 26004251 DOI: 10.1016/j.virol.2015.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 03/15/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 12/19/2022]
Abstract
We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3'-N-P-P3-M-G-P6-L-5'. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3' leader and 5' trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino a 60 Cuadras k 5,5, Córdoba X5020ICA, Argentina; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Fabián Giolitti
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino a 60 Cuadras k 5,5, Córdoba X5020ICA, Argentina
| | - Soledad de Breuil
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino a 60 Cuadras k 5,5, Córdoba X5020ICA, Argentina
| | - Verónica Trucco
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino a 60 Cuadras k 5,5, Córdoba X5020ICA, Argentina
| | - Claudia Nome
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino a 60 Cuadras k 5,5, Córdoba X5020ICA, Argentina
| | - Sergio Lenardon
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria (INTA), Camino a 60 Cuadras k 5,5, Córdoba X5020ICA, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
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