1
|
Singh J, Teotia S, Singh AK, Arya M, Rout AK, Behera BK, Majumder S. Whole genome sequence analysis of shallot virus X from India reveals it to be a natural recombinant with positive selection pressure. BMC Genom Data 2024; 25:42. [PMID: 38711021 DOI: 10.1186/s12863-024-01196-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/23/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Shallots are infected by various viruses like Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV) and Shallot virus X (ShVX). In India, they have been found to be persistently infected by ShVX. ShVX also infects onion and garlic in combination with other carlaviruses and potyviruses. ShVX is a member of genus Allexivirus of family Alphaflexiviridae. ShVX has a monopartite genome, which is represented by positive sense single-stranded RNA. Globally, only six complete and 3 nearly complete genome sequences of ShV X are reported to date. This number is insufficient to measure a taxon's true molecular diversity. Moreover, the complete genome sequence of ShVX from Asia has not been reported as yet. Therefore, this study was undertaken to generate a complete genome sequence of ShVX from India. RESULTS Shallot virus X (ShVX) is one of the significant threats to Allium crop production. In this study, we report the first complete genome sequence of the ShVX from India through Next-generation sequencing (NGS). The complete genome of the ShVX (Accession No. OK104171), from this study comprised 8911 nucleotides. In-silico analysis of the sequence revealed variability between this isolate and isolates from other countries. The dissimilarities are spread all over the genome specifically some non-coding intergenic regions. Statistical analysis of individual genes for site-specific selection indicates a positive selection in NABP region. The presence of a recombination event was detected in coat protein region. The sequence similarity percentage and phylogenetic analysis indicate ShVX Indian isolate is a distinctly different isolate. Recombination and site-specific selection may have a function in the evolution of this isolate. This is the first detailed study of the ShVX complete genome sequence from Southeast Asia. CONCLUSION This study presents the first report of the entire genome sequence of an Indian isolate of ShVX along with an in-depth exploration of its evolutionary traits. The findings highlight the Indian variant as a naturally occurring recombinant, emphasizing the substantial role of recombination in the evolution of this viral species. This insight into the molecular diversity of strains within a specific geographical region holds immense significance for comprehending and forecasting potential epidemics. Consequently, the insights garnered from this research hold practical value for shaping ShVX management strategies and providing a foundation for forthcoming studies delving into its evolutionary trajectory.
Collapse
Affiliation(s)
- Jyoti Singh
- Department of Biotechnology, Sharda University, Greater Noida, India
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida, India
| | - Ajay Kumar Singh
- Deaprtment of Bioinformatics, Central University of South Bihar, Gaya, Bihar, India
| | - Meenakshi Arya
- Rani Lakshmi Bai Central Agricultural University, 284003, Jhansi, Uttar Pradesh, India.
| | - Ajaya Kumar Rout
- Rani Lakshmi Bai Central Agricultural University, 284003, Jhansi, Uttar Pradesh, India
| | - Bijay Kumar Behera
- Rani Lakshmi Bai Central Agricultural University, 284003, Jhansi, Uttar Pradesh, India
| | - Shahana Majumder
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Motihari, Bihar, India.
| |
Collapse
|
2
|
Eichmeier A, Peňázová E, Čechová J, Berraf-Tebbal A. Survey and Diversity of Grapevine Pinot gris virus in Algeria and Comprehensive High-Throughput Small RNA Sequencing Analysis of Two Isolates from Vitis vinifera cv. Sabel Revealing High Viral Diversity. Genes (Basel) 2020; 11:genes11091110. [PMID: 32971929 PMCID: PMC7563602 DOI: 10.3390/genes11091110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/25/2020] [Revised: 09/08/2020] [Accepted: 09/16/2020] [Indexed: 01/24/2023] Open
Abstract
Grapevine Pinot gris virus (GPGV) is a putative causal agent of grapevine leaf mottling and deformation disease that has been reported worldwide throughout the grapevine-growing regions. Fifty-four grapevines collected from five Algerian grapevine-growing regions were tested for the presence of GPGV in phloem tissues. Eight of the tested grapevines were infected by GPGV. Viromes of two selected Vitis vinifera cv. Sabel grapevines infected by GPGV and showing virus-like symptoms were analyzed by small RNA sequencing. Phylogenetic analyses of the partial coding sequence (cds) of the RNA-dependent RNA polymerase (RdRp) domain showed that all Algerian GPGV isolates were grouped with some already-described asymptomatic isolates. This study provides the first survey of the occurrence of GPGV in Algeria. Moreover, Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine virus B, Grapevine rupestris vein feathering virus, Hop stunt viroid and Grapevine yellow speckle viroid 1 were detected in Algeria for the first time.
Collapse
|
3
|
Park D, Goh CJ, Lee JS, Sebastiani F, Hahn Y. Identification of Pistacia-associated flexivirus 1, a putative mycovirus of the family Gammaflexiviridae, in the mastic tree (Pistacia lentiscus) transcriptome. Acta Virol 2020; 64:28-35. [PMID: 32180416 DOI: 10.4149/av_2020_104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study, we identified the genome sequence of the novel virus Pistacia-associated flexivirus 1 (PAFV1), a putative member of the mycovirus family Gammaflexiviridae (the order Tymovirales), via analysis of a transcriptome dataset for the mastic tree (Pistacia lentiscus, the family Anacardiaceae). PAFV1 was predicted to have three open reading frames (ORFs): ORF1, encoding a replicase (REP) with RNA-dependent RNA polymerase activity; ORF2, a movement protein (MP); and ORF3, a hypothetical protein. The PAFV1 REP sequence showed high similarity to those of three known members of the family Gammaflexiviridae i.e., Entoleuca gammaflexivirus 1 (EnFV1), Entoleuca gammaflexivirus 2 (EnFV2), and Botrytis virus F (BVF). A genome contig of the fungus Monosporascus cannonballus also contained a sequence of an endogenous virus similar to that of PAFV1. Sequence comparison and phylogenetic analysis indicated that PAFV1, EnFV1, and the endogenous virus of M. cannonballus formed a distinct subgroup (apart from EnFV2 and BVF), and may be the founding members of a novel genus in the family Gammaflexiviridae. Notably, MP sequences of PAFV1/EnFV1 showed similarity to the MP sequences of the mycovirus group called tobamo-like mycoviruses (an unassigned taxon), implying that genomic recombination occurred between members of the family Gammaflexiviridae and tobamo-like mycoviruses. Since PAFV1 is phylogenetically related to mycoviruses, PAFV1 may also be a mycovirus that infected a fungus associated with the mastic tree sample, which is evidenced by the presence of fungal ribosomal RNA sequences in the mastic tree transcriptome. Thus, the PAFV1 genome sequence may be useful in elucidating the genome evolution of Gammaflexiviridae and tobamo-like mycoviruses. Keywords: Pistacia-associated flexivirus 1; Gammaflexiviridae; mycovirus, mastic tree.
Collapse
|
4
|
Marais A, Šafářová D, Navrátil M, Faure C, Cornaggia D, Brans Y, Suchá J, Candresse T. Complete genome sequence of cherry virus T, a novel cherry-infecting tepovirus. Arch Virol 2020; 165:1711-1714. [PMID: 32409875 DOI: 10.1007/s00705-020-04656-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 02/24/2020] [Accepted: 04/12/2020] [Indexed: 10/24/2022]
Abstract
Double-stranded RNA and total RNA purified from sour cherry leaves (Prunus cerasus, cv. Amarelka Chvalkovicka) was analyzed by high-throughput sequencing. BLAST annotation identified contigs with homology to several already known cherry-infecting viruses (prune dwarf virus, prunus necrotic ringspot virus, prunus virus F, little cherry virus 1) as well as contigs with sequences more distantly related to those of members of the family Betaflexiviridae and in particular to prunus virus T of the genus Tepovirus. The full genome sequence of a putative virus (6,847 nucleotides [nt]; GenBank no. MT090966) was assembled and completed at the genome ends. The genome has a typical tepovirus organization, containing three overlapping open reading frames (ORFs), encoding a replication-associated protein, a movement protein and a capsid protein, respectively. Both its genome organization and its phylogenetic relationships show that the virus belongs to the genus Tepovirus, but considering the species demarcation criteria for the family Betaflexiviridae, it appears to represent a novel virus species, and we propose the name "cherry virus T" (ChVT) for this virus.
Collapse
Affiliation(s)
- A Marais
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - D Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - M Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - C Faure
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - D Cornaggia
- Laboratoire de Virologie et de Biologie moléculaire, CTIFL, 28 Route des Nébouts, 24130, Prigonrieux, France
| | - Y Brans
- Laboratoire de Virologie et de Biologie moléculaire, CTIFL, 28 Route des Nébouts, 24130, Prigonrieux, France
| | - J Suchá
- Research Institute of Pomology in Holovousy Ltd, Holovousy 129, 508 01, Hořice, Czech Republic
| | - T Candresse
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.
| |
Collapse
|
5
|
Zheng L, Chen M, Li R. Camellia ringspot-associated virus 4, a proposed new foveavirus from Camellia japonica. Arch Virol 2020; 165:1707-1710. [PMID: 32409876 DOI: 10.1007/s00705-020-04655-x] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/11/2020] [Indexed: 01/23/2023]
Abstract
One large contig with high sequence similarity to Asian prunus virus 2 was identified by high-throughput sequencing from a camellia (Camellia japonica) tree with ringspot symptoms. The complete genome of this new virus was determined to be 8829 nucleotides long, excluding the 3' poly(A) tail. Its genome organization resembles that of known foveaviruses but contains an additional open reading frame in the 3'-terminal region. Phylogenetic analysis also places this virus with members of the genus Foveavirus in the family Betaflexiviridae in the same subgroup. The virus, which is provisionally named "camellia ringspot-associated virus 4″, shares 50-56% nucleotide sequence identity with other foveaviruses and should represent a new species in the genus.
Collapse
Affiliation(s)
- Luping Zheng
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Madeleine Chen
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.
| |
Collapse
|
6
|
Tan SH, Osman F, Bodaghi S, Dang T, Greer G, Huang A, Hammado S, Abu-Hajar S, Campos R, Vidalakis G. Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay. PLoS One 2019; 14:e0223958. [PMID: 31622412 PMCID: PMC6797102 DOI: 10.1371/journal.pone.0223958] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 06/10/2019] [Accepted: 09/18/2019] [Indexed: 12/05/2022] Open
Abstract
Citrus tatter leaf virus (CTLV) threatens citrus production worldwide because it induces bud-union crease on the commercially important Citrange (Poncirus trifoliata × Citrus sinensis) rootstocks. However, little is known about its genomic diversity and how such diversity may influence virus detection. In this study, full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside, were characterized using next generation sequencing. Genome structure and sequence for all CTLV isolates were similar to Apple stem grooving virus (ASGV), the type species of Capillovirus genus of the Betaflexiviridae family. Phylogenetic analysis highlighted CTLV’s point of origin in Asia, the virus spillover to different plant species and the bottleneck event of its introduction in the United States of America (USA). A reverse transcription quantitative polymerase chain reaction assay was designed at the most conserved genome area between the coat protein and the 3’-untranslated region (UTR), as identified by the full genome analysis. The assay was validated with different parameters (e.g. specificity, sensitivity, transferability and robustness) using multiple CTLV isolates from various citrus growing regions and it was compared with other published assays. This study proposes that in the era of powerful affordable sequencing platforms the presented approach of systematic full-genome sequence analysis of multiple virus isolates, and not only a small genome area of a small number of isolates, becomes a guideline for the design and validation of molecular virus detection assays, especially for use in high value germplasm programs.
Collapse
Affiliation(s)
- Shih-hua Tan
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Greg Greer
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Amy Huang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Sarah Hammado
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Shurooq Abu-Hajar
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Roya Campos
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
| |
Collapse
|
7
|
Diaz-Lara A, Brisbane RS, Aram K, Golino D, Al Rwahnih M. Detection of new vitiviruses infecting grapevine in California. Arch Virol 2019; 164:2573-2580. [PMID: 31346770 DOI: 10.1007/s00705-019-04355-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 02/06/2019] [Accepted: 06/03/2019] [Indexed: 11/25/2022]
Abstract
Recently, five new viruses from the genus Vitivirus were identified and named grapevine virus G, H, I, J and L. These viruses were targeted in a survey to evaluate their prevalence in different grapevine populations in California. Excluding a single detection of GVJ, other vitiviruses were detected infecting several grapevine selections via RT-PCR and later confirmed by sequencing. This paper represents the first report of GVG, GVH and GVI in California. In a preliminary analysis, the sequence diversity between identified isolates of GVG, GVH, GVI and GVL was investigated using distance matrices and phylogenetics. Finally, coinfections involving diverse vitiviruses and leafroll viruses were evidenced.
Collapse
Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Reid S Brisbane
- Foundation Plant Services, University of California-Davis, Davis, CA, 95616, USA
| | - Kamyar Aram
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA.
| |
Collapse
|
8
|
Marais A, Faure C, Theil S, Candresse T. Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France. PLoS One 2019; 14:e0219024. [PMID: 31339882 PMCID: PMC6655591 DOI: 10.1371/journal.pone.0219024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/09/2019] [Indexed: 11/19/2022] Open
Abstract
To elucidate the etiology of a new disease of shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed using high-throughput sequencing (HTS). Annotation of contigs, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch's postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.
Collapse
Affiliation(s)
- Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| |
Collapse
|
9
|
Svanella-Dumas L, Τsarmpopoulos Ι, Marais A, Theil S, Faure C, Gaudin J, Candresse T. Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France. Arch Virol 2018; 163:2543-2545. [PMID: 29730706 DOI: 10.1007/s00705-018-3858-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 02/28/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
Double-stranded RNAs purified from cultivated (Lactuca sativa) or wild (L. serriola) lettuce from southwest France were analyzed by high-throughput sequencing. For both samples, BLAST annotation revealed contigs with homology to Betaflexiviridae family members. The full genome sequence of the isolate from cultivated lettuce (JG1) was completed (8,536 nucleotides [nt], excluding the poly(A) tail). The sequence of the 3' half of the genome (4,800 nt) of a wild lettuce isolate (P22) was determined and found to share 95.1% nt sequence identity with the JG1 isolate. The JG1 genome contains four open reading frames, encoding a replicase, a movement protein, a capsid protein, and a protein of unknown function, respectively. Based on genome organization and phylogenetic relationships, the lettuce virus is most closely related to the recently described carrot chordoviruses 1 and 2 in the family Betaflexiviridae. Considering the species demarcation criteria in this family, the two lettuce viruses represent isolates of a new chordovirus species for which the name "lettuce chordovirus 1" (LeCV1) is proposed.
Collapse
Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Ιason Τsarmpopoulos
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Jonathan Gaudin
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
| |
Collapse
|
10
|
Goh CJ, Park D, Kim H, Sebastiani F, Hahn Y. Novel Divavirus (the family Betaflexiviridae) and Mitovirus (the family Narnaviridae) species identified in basil (Ocimum basilicum). Acta Virol 2018; 62:304-309. [PMID: 30160146 DOI: 10.4149/av_2018_224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transcriptome data obtained from a plant sample often contain a large number of reads that are derived from associated RNA virus genomes that were co-isolated during RNA preparation. These virus-derived reads can be assembled into a novel plant RNA genome sequence. Here, a basil (Ocimum basilicum) transcriptome dataset was analyzed to identify two new RNA viruses, which were named Ocimum basilicum RNA virus 1 (ObRV1) and Ocimum basilicum RNA virus 2 (ObRV2). A phylogenetic analysis of the ObRV1 RNA-dependent RNA polymerase (RdRp) motif indicated that ObRV1 is a novel species of the genus Divavirus of the family Betaflexiviridae. ObRV1 is the fourth divavirus species to be identified. The ObRV2 RdRp motif showed sequence similarity to viruses of the genus Mitovirus of the family Narnaviridae, which infect fungal mitochondria. Although most of the known mitoviruses do not produce a functional RdRp using the plant mitochondrial genetic code, the ObRV2 encodes a full-length RdRp using both the fungal and plant mitochondrial genetic codes.
Collapse
|
11
|
Beuve M, Hily JM, Alliaume A, Reinbold C, Le Maguet J, Candresse T, Herrbach E, Lemaire O. A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms. Arch Virol 2018; 163:2937-2946. [PMID: 30033497 DOI: 10.1007/s00705-018-3949-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 04/24/2018] [Accepted: 05/11/2018] [Indexed: 11/25/2022]
Abstract
We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.
Collapse
Affiliation(s)
- Monique Beuve
- SVQV, Université de Strasbourg, 68000, Colmar, France
| | | | | | | | - Jean Le Maguet
- SVQV, Université de Strasbourg, 68000, Colmar, France
- Institut Français des Productions Cidricoles (IFPC), 61500, Sées, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon Cedex, France
| | | | | |
Collapse
|
12
|
Baráth D, Jaksa-Czotter N, Molnár J, Varga T, Balássy J, Szabó LK, Kirilla Z, Tusnády GE, Preininger É, Várallyay É. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. Viruses 2018; 10:E318. [PMID: 29891760 PMCID: PMC6024520 DOI: 10.3390/v10060318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 05/11/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 12/14/2022] Open
Abstract
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation.
Collapse
Affiliation(s)
- Dániel Baráth
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - János Molnár
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, 7632 Pécs, Hungary.
| | - Tünde Varga
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | - Júlia Balássy
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - Zoltán Kirilla
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Gábor E Tusnády
- Institute of Enzymology, Research Center of Natural Sciences, HAS, 1117 Budapest, Hungary.
| | - Éva Preininger
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Éva Várallyay
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| |
Collapse
|
13
|
Yoshida N, Shimura H, Masuta C. Allexiviruses may have acquired inserted sequences between the CP and CRP genes to change the translation reinitiation strategy of CRP. Arch Virol 2018; 163:1419-1427. [PMID: 29417240 DOI: 10.1007/s00705-018-3749-2] [Citation(s) in RCA: 2] [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: 11/26/2017] [Accepted: 01/17/2018] [Indexed: 11/28/2022]
Abstract
Allexiviruses are economically important garlic viruses that are involved in garlic mosaic diseases. In this study, we characterized the allexivirus cysteine-rich protein (CRP) gene located just downstream of the coat protein (CP) gene in the viral genome. We determined the nucleotide sequences of the CP and CRP genes from numerous allexivirus isolates and performed a phylogenetic analysis. According to the resulting phylogenetic tree, we found that allexiviruses were clearly divided into two major groups (group I and group II) based on the sequences of the CP and CRP genes. In addition, the allexiviruses in group II had distinct sequences just before the CRP gene, while group I isolates did not. The inserted sequence between the CP and CRP genes was partially complementary to garlic 18S rRNA. Using a potato virus X vector, we showed that the CRPs affected viral accumulation and symptom induction in Nicotiana benthamiana, suggesting that the allexivirus CRP is a pathogenicity determinant. We assume that the inserted sequences before the CRP gene may have been generated during viral evolution to alter the termination-reinitiation mechanism for coupled translation of CP and CRP.
Collapse
Affiliation(s)
- Naoto Yoshida
- Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Hanako Shimura
- Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan.
| | - Chikara Masuta
- Graduate School of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| |
Collapse
|
14
|
Morán F, Olmos A, Lotos L, Predajňa L, Katis N, Glasa M, Maliogka V, Ruiz-García AB. A novel specific duplex real-time RT-PCR method for absolute quantitation of Grapevine Pinot gris virus in plant material and single mites. PLoS One 2018; 13:e0197237. [PMID: 29763449 PMCID: PMC5953474 DOI: 10.1371/journal.pone.0197237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/28/2018] [Indexed: 11/19/2022] Open
Abstract
Grapevine Pinot gris virus (GPGV) is a widely distributed grapevine pathogen that has been associated to the grapevine leaf mottling and deformation disease. With the aim of better understanding the disease epidemiology and providing efficient control strategies a specific and quantitative duplex TaqMan real-time RT-PCR assay has been developed. This method has allowed reliable quantitation of the GPGV titer ranging from 30 up to 3 x 108 transcript copies, with a detection limit of 70 viral copies in plant material. The assay targets a grapevine internal control that reduces the occurrence of false negative results, thus increasing the diagnostic sensitivity of the technique. Viral isolates both associated and non-associated to symptoms from Greece, Slovakia and Spain have been successfully detected. The method has also been applied to the absolute quantitation of GPGV in its putative transmission vector Colomerus vitis. Moreover, the viral titer present in single mites has been determined. In addition, in the current study a new polymorphism in the GPGV genome responsible for a shorter movement protein has been found. A phylogenetic study based on this genomic region has shown a high variability among Spanish isolates and points to a different evolutionary origin of this new polymorphism. The methodology here developed opens new possibilities for basic and epidemiological studies as well as for the establishment of efficient control strategies.
Collapse
Affiliation(s)
- Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Leonidas Lotos
- Aristotle University of Thessaloniki, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Laboratory, Thessaloniki, Greece
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
| | - Nikolaos Katis
- Aristotle University of Thessaloniki, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Laboratory, Thessaloniki, Greece
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava, Slovakia
| | - Varvara Maliogka
- Aristotle University of Thessaloniki, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Laboratory, Thessaloniki, Greece
| | - Ana B. Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- * E-mail:
| |
Collapse
|
15
|
Guo W, Zheng W, Wang M, Li X, Ma Y, Dai H. Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China. PLoS One 2016; 11:e0161099. [PMID: 27519059 PMCID: PMC4982687 DOI: 10.1371/journal.pone.0161099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/31/2016] [Indexed: 11/19/2022] Open
Abstract
The genome sequences of Apple chlorotic leaf spot virus (ACLSV) isolates from three accessions of hawthorns (Crataegus pinnatifida) grown at Shenyang Agricultural University were determined using Illumina RNA-seq. To confirm the assembly data from the de novo sequencing, two ACLSV genomic sequences (SY01 and SY02) were sequenced using the Sanger method. The SY01 and SY02 sequences obtained with the Sanger method showed 99.5% and 99.7% nucleotide identity with the transcriptome data, respectively. The genome sequences of the hawthorn isolates SY01, SY02 and SY03 (GenBank accession nos. KM207212, KU870524 and KU870525, respectively) consisted of 7,543, 7,561 and 7,545 nucleotides, respectively, excluding poly-adenylated tails. Sequence analysis revealed that these hawthorn isolates shared an overall nucleotide identity of 82.8–92.1% and showed the highest identity of 90.3% for isolate YH (GenBank accession no. KC935955) from pear and the lowest identity of 67.7% for isolate TaTao5 (GenBank accession no. EU223295) from peach. Hawthorn isolate sequences were similar to those of ‘B6 type’ ACLSV. The relationship between ACLSV isolates largely depends upon the host species. This represents the first comparative study of the genome sequences of ACLSV isolates from hawthorns.
Collapse
Affiliation(s)
- Wei Guo
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Wenyan Zheng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Mei Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Xiaohong Li
- College of Agronomy, Eastern Liaoning University, 325 Wenhua Road, Dandong, Liaoning, 118003, China
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
| | - Hongyan Dai
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, Liaoning, 110866, China
- * E-mail:
| |
Collapse
|
16
|
Fan X, Hong N, Zhang Z, Yang Z, Ren F, Hu G, Li Z, Zhou J, Dong Y, Wang G. Identification of a divergent variant of grapevine berry inner necrosis virus in grapevines showing chlorotic mottling and ring spot symptoms. Arch Virol 2016; 161:2025-7. [PMID: 27068163 DOI: 10.1007/s00705-016-2856-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 12/28/2015] [Accepted: 03/29/2016] [Indexed: 12/13/2022]
Abstract
A new variant of grapevine berry inner necrosis virus (GINV) was identified by sequencing of small RNA extracted from 'Beta' and Thompson seedless grapevines showing leaf mottle and ring spot symptoms. However, GINV was not found in symptomless samples used as a control. The complete genome sequences of two GINV isolates (KU234316-17) were determined, and these showed 75.76-89.74% sequence identity to the genome of a previously reported Japanese GINV isolate. The new variants appear to be evolutionarily distinct from the original GINV isolate. This is the first report of GINV outside of Japan.
Collapse
Affiliation(s)
- Xudong Fan
- National Key Laboratory of Agromicrobiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China
| | - Ni Hong
- National Key Laboratory of Agromicrobiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Zunping Zhang
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China
| | - Zuokun Yang
- National Key Laboratory of Agromicrobiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Fang Ren
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China
| | - Guojun Hu
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China
| | - Zhengnan Li
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China
| | - Jun Zhou
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China
| | - Yafeng Dong
- National Center for Eliminating Viruses from Deciduous Fruit Tree, Research Institute of Pomology, Chinese Academy of Agriculture Sciences, Liaoning, 125100, Xingcheng, People's Republic of China.
| | - Guoping Wang
- National Key Laboratory of Agromicrobiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
| |
Collapse
|
17
|
Zhen S, Kurth EG, Peremyslov VV, Changyong Z, Dolja VV. Molecular characterization of a citrus yellow vein clearing virus strain from China. Arch Virol 2015; 160:1811-3. [PMID: 25913691 DOI: 10.1007/s00705-015-2423-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 12/11/2014] [Accepted: 04/04/2015] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequence of an isolate of citrus yellow vein clearing virus from Yunnan, China (CYVCV-RL), was determined following whole-genome amplification by RT-PCR. The CYVCV-RL genome was 7529 nt in length, excluding the 3' poly (A) tail, and contained six open reading frames (ORFs), resembling that of viruses belonging to the genus Mandarivirus in the family Alphaflexiviridae. Sequence analysis showed that the CYVCV-RL shared the greatest nucleotide sequence identity with the CYVCV-Y1 (JX040635) isolate from Turkey for the whole genome (97.1%), 5' UTR (98.7%), 3' UTR (100.0%), and each of six ORFs (96.5% to 97.8%), suggesting that there is apparent genetic stability among CYVCV isolates of different geographic origin.
Collapse
Affiliation(s)
- Song Zhen
- Citrus Research Institute of Southwest University, Chongqing, 400712, People's Republic of China
| | | | | | | | | |
Collapse
|
18
|
Saldarelli P, Giampetruzzi A, Morelli M, Malossini U, Pirolo C, Bianchedi P, Gualandri V. Genetic Variability of Grapevine Pinot gris virus and Its Association with Grapevine Leaf Mottling and Deformation. Phytopathology 2015; 105:555-563. [PMID: 25423070 DOI: 10.1094/phyto-09-14-0241-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The role of Grapevine Pinot gris virus (GPGV) in the etiology of grapevine leaf mottling and deformation was investigated by biological and molecular assays. A survey on different cultivars from the Trentino Region in Italy showed a widespread distribution of GPGV, which was associated with symptomatic (79%) but also with symptomless (21%) vines. Symptomatic and GPGV-infected 'Pinot gris' vines induced symptoms on grafted vines of healthy Pinot gris or 'Traminer', whereas GPGV-infected but symptomless vines did not. High-throughput sequencing of small RNA (sRNA) populations of two infected Pinot gris accessions confirmed the existence of nearly overlapping viromes in vines with or without symptoms but phylogenetic analyses of the genomes of seven GPGV isolates from Italy and the Czech and Slovak Republics clearly differentiated those infecting symptomatic vines. The involvement of Grapevine rupestris vein feathering virus (GRVFV) in the disease, which was only infecting the symptomatic vine, was ruled out by reverse-transcription polymerase chain reaction studies. Maximum likelihood and Bayesian phylogenetic analysis of two GPGV genomic regions, encompassing part of the movement protein (MP) and coat protein gene sequences and the RNA-dependent RNA polymerase domain of the replicase gene, showed that isolates from symptomatic vines form a lineage distinct from that of symptomless vines. Moreover, the presence or lack of the MP stop codon identified in viral isolates from symptomatic or symptomless vines, respectively, is likely responsible for an MP six amino acids longer in symptomless isolates.
Collapse
Affiliation(s)
- P Saldarelli
- First, second, third, and fifth authors: CNR Istituto per la Protezione Sostenibile delle Piante, UOS-Bari, and Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari via Amendola 165/A, 70126, Bari, Italy; and fourth, sixth, and seventh authors: FEM-IASMA, Centre for Technology Transfer, via E. Mach 1, 38010, San Michele all'Adige (Trento), Italy
| | | | | | | | | | | | | |
Collapse
|
19
|
Chen H, Chen S, Li Y, Ye T, Hao L, Fan Z, Guo L, Zhou T. Phylogenetic analysis and recombination events in full genome sequences of apple stem grooving virus. Acta Virol 2015; 58:309-16. [PMID: 25518711 DOI: 10.4149/av_2014_04_309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Apple stem grooving virus (ASGV) is one of the most important viral pathogens infecting pome and stone fruit trees worldwide. In this study, with the complete nucleotide sequence of isolate ASGV-T47, which we generated, molecular variation and recombination in ASGV full genomic sequences worldwide were analyzed. ASGV-T47 shared 79.7-97.6% nucleotide identity with the other isolates worldwide and had the highest identity with an isolate from Japan. Phylogenetic analysis based on whole genome clustered all 16 isolates from around the world into two groups with no correlation to host or geographical origin. Four isolates were detected to be recombinants. Selection pressure estimation indicated that the two codons at positions 1756 and 1798 are under positive selection, while purifying selection is the primary evolutionary dynamics for ASGV.
Collapse
|
20
|
Abstract
A new genetic variant of grapevine virus A (GVA) of phylogenetic group I was identified during comparative analysis of the viruses infecting two sibling grapevines cv. Shiraz. The grapevines were propagated from a single mother plant. One of them become infected with Shiraz disease (SD), which is highly destructive on noble grapevine cultivars Shiraz and Merlot in South Africa. The new variant was not associated with SD, as it was present in both SD-affected and SD-free plants. However, unlike in an earlier study of grapevines affected by this disease, this GVA variant of group I strongly dominated over a coinfecting variant of group II associated with SD and a variant of group III. The variant, named I327-5, was mechanically transmitted from SD-affected grapevine to Nicotiana benthamiana, and its genome was fully sequenced. The sequence data revealed that the most distinctive genomic feature of variant I327-5 is the deletion of three nucleotides in the region where the ORF2 and ORF3 genes overlap. These genes of GVA encode a 19.8-kDa protein, the function of which remains unknown, and a 31-kDa protein that is indispensable for the movement of the virus in plants. An alignment of the amino acid sequences of these proteins encoded by variant I327-5 with the corresponding proteins encoded by other members of group I suggested that, as the result of mutations, a neutral threonine or alanine and a negatively charged glutamic acid, respectively, were removed from the proteins of GVA variant I327-5.
Collapse
Affiliation(s)
- D E Goszczynski
- Plant Protection Research Institute, Agricultural Research Council, Private Bag X134, Queenswood, Pretoria, 0121, South Africa,
| |
Collapse
|
21
|
Alabi OJ, Al Rwahnih M, Mekuria TA, Naidu RA. Genetic diversity of Grapevine virus A in Washington and California vineyards. Phytopathology 2014; 104:548-560. [PMID: 24168043 DOI: 10.1094/phyto-06-13-0179-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Grapevine virus A (GVA; genus Vitivirus, family Betaflexiviridae) has been implicated with the Kober stem grooving disorder of the rugose wood disease complex. In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.
Collapse
|
22
|
Blouin AG, Chavan RR, Pearson MN, MacDiarmid RM, Cohen D. Detection and characterisation of two novel vitiviruses infecting Actinidia. Arch Virol 2012; 157:713-22. [PMID: 22274622 DOI: 10.1007/s00705-011-1219-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [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: 08/05/2011] [Accepted: 11/30/2011] [Indexed: 10/14/2022]
Abstract
Two co-infecting novel vitiviruses from Actinidia chinensis were identified from mechanically inoculated Nicotiana occidentalis. Both virus genomes were sequenced and share 64% nucleotide identity. Their overall structure is typical of vitiviruses, with five open reading frames (ORFs) and a polyadenylated 3' end. Open reading frame 4 (ORF4) encodes the coat protein, the most conserved gene of the vitiviruses, in which they share 75% amino acid identity, 61-68% with grapevine virus B, 55-59% with grapevine virus A, and 37-42% with grapevine virus E. Based on the molecular criteria for species demarcation in the family Betaflexiviridae, these are two novel viruses, tentatively named Actinidia virus A and Actinidia virus B.
Collapse
Affiliation(s)
- Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand.
| | | | | | | | | |
Collapse
|
23
|
Goszczynski DE. Divergent molecular variants of Grapevine virus B (GVB) from corky bark (CB)-affected and CB-negative LN33 hybrid grapevines. Virus Genes 2010; 41:273-81. [PMID: 20628801 DOI: 10.1007/s11262-010-0511-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [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: 04/28/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
Abstract
Analysis of two Grapevine virus B (GVB)-infected LN33 hybrid grapevines revealed that a plant exhibiting clear symptoms of corky bark (CB) disease was infected with two molecular variants of the virus, whereas a plant exhibiting no disease symptoms was infected with only one variant. Sequence results indicated that the single variant in the CB-negative grapevine was also one of the two present in the CB-affected hybrid. Plant extracts from these two grapevines were used to successfully transmit the virus to N. benthamiana. After further cloning and sequencing, two clearly divergent variants were identified. Comparative molecular analysis of the variants, named here GVB 953-1 and GVB-H1, respectively, transmitted from CB-affected and consistently CB-negative plants, revealed short genomic regions, most of them highly divergent, that encoded amino acid sequences, containing significant amino acid substitutions altering the net charges of their respective proteins. Interestingly, a comparison of these variants to genome sequence data of GVB variants GVB Italy and GVB 94/971 available from the GenBank, revealed that these significant amino acid substitutions were the same for, and unique to, the variant pairs GVB 953-1/GVB Italy and GVB-H1/GVB 94/971. This despite the variants of each pair being otherwise clearly different at nucleotide and amino acid levels. In addition, both sets of variants differed substantially in their respective 3'-non-translated (3'NTR) regions. The relevance of these findings is discussed.
Collapse
Affiliation(s)
- Dariusz E Goszczynski
- Plant Protection Research Institute, Agricultural Research Council, Pretoria, Republic of South Africa.
| |
Collapse
|
24
|
Abstract
LN33 grapevine plants were artificially inoculated with budwoods originating from a field-cultivated Traminer grapevine which was naturally infected with Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine virus A (GVA), Grapevine virus B (GVB), Rupestris stem pitting-associated virus (RSPaV), and an unclassified tymovirus. Four years after inoculation, a comparison of the cane weights between healthy and infected grapevines did not show any significant difference. Corky bark symptoms or destructive effects of GVB infection never appeared on the infected grapevines. Dormant canes, sampled before the beginning of the vegetation period, were used for detection of grapevine viruses by ELISA or RT-PCR. ELISA turned out unexpectedly to be more effective than RT-PCR for detecting GLRaV-1 probably due to an insufficient specificity of the primers used, not reflecting the actual genetic variability of the virus. Distribution of viruses in the infected grapevines showed a different degree of irregularity in dependence on individual viruses. Therefore, in order to properly verify the sanitary status of grapevines under testing, several random samples from different parts of a tested plant have to be analyzed.
Collapse
Affiliation(s)
- P Kominek
- Crop Research Institute, Prague-Ruzyne, Czech Republic.
| | | | | |
Collapse
|
25
|
Panattoni A, D'Anna F, Cristani C, Triolo E. Grapevine vitivirus A eradication in Vitis vinifera explants by antiviral drugs and thermotherapy. J Virol Methods 2007; 146:129-35. [PMID: 17645950 DOI: 10.1016/j.jviromet.2007.06.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [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: 03/28/2007] [Revised: 06/05/2007] [Accepted: 06/11/2007] [Indexed: 11/23/2022]
Abstract
Grapevine shoot cultures infected by Grapevine vitivirus A (GVA) were grown on Quorin-Lepoivre basic medium and submitted to in vitro chemotherapy and thermotherapy sanitation techniques. Ribavirin (Rb) at 20gml(-1), dihydroxypropyladenine (DHPA) at 60gml(-1) and their combination (RbDH) were added to the proliferating medium for three subsequent subcultures of 30 days each. Phytotoxicity was observed on drug-treated plantlets, which displayed a high percentage of mortality for each drug at doses higher than those aforementioned. Sequential ELISA were performed at the end of each subculture and ELISA-negative explants were submitted to RT-PCR. ELISA showed no antiviral activity following DHPA administration. Rb and RbDH treatment produced ELISA-negative explants which were assayed by RT-PCR and nested PCR. Biomolecular results showed no virus eradication in Rb treated explants but RbDH administration generated a percentage (40.0%) of GVA-free plantlets that permitted restoration of a new healthy generation of explants. Sixty percent (60%) of GVA eradication as confirmed by RT-PCR was obtained by in vitro thermotherapy at 36 degrees C for 57 days.
Collapse
Affiliation(s)
- Alessandra Panattoni
- Department of Tree Science, Entomology and Plant Pathology G. Scaramuzzi, University of Pisa, Italy.
| | | | | | | |
Collapse
|
26
|
Kang SG, Koo BJ, Lee ET, Chang MU. Allexivirus transmitted by eriophyid mites in garlic plants. J Microbiol Biotechnol 2007; 17:1833-1840. [PMID: 18092468] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Viruses in garlic plants (Allium sativum L.) have accumulated and evolved over generations, resulting in serious consequences for the garlic trade around the world. These viral epidemics are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses. However, little is known about viral epidemics in garlic plants caused by eriophyid mites. Therefore, this study investigated the infection of garlic plants with Allexiviruses by eriophyid mites. When healthy garlic plants were cocultured with eriophyid mites, the leaves of the garlic plants developed yellow mosaic strips and became distorted. In extracts from the eriophyid mites, Allexiviruses were observed using immunosorbent electron microscopy (ISEM). From an immunoblot analysis, coat proteins against an Allexivirus garlic-virus antiserum were clearly identified in purified extracts from collected viral-infected garlic plants, eriophyid mites, and garlic plants infected by eriophyid mites. A new strain of GarV-B was isolated and named GarV-B Korea isolate 1 (GarV-B1). The ORF1 and ORF2 in GarV-B1 contained a typical viral helicase, RNA-directed RNA polymerase (RdRp), and triple gene block protein (TGBp) for viral movement between cells. The newly identified GarV-B1 was phylogenetically grouped with GarV-C and GarV-X in the Allexivirus genus. All the results in this study demonstrated that eriophyid mites are a transmitter insect species for Allexiviruses.
Collapse
Affiliation(s)
- Sang Gu Kang
- Molecular Genetics Laboratory, Department of Biotechnology, School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
| | | | | | | |
Collapse
|
27
|
Tzanetakis IE, Postman JD, Martin RR. Identification, detection and transmission of a new vitivirus from Mentha. Arch Virol 2007; 152:2027-33. [PMID: 17680328 DOI: 10.1007/s00705-007-1030-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [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: 01/23/2007] [Accepted: 06/12/2007] [Indexed: 11/27/2022]
Abstract
Mentha x gracilis 'Variegata' is an ornamental clone with a phenotype caused by virus infection. Several clones were ordered from mail-order nurseries in an attempt to identify a virus consistently associated with symptoms. One of these clones did not exhibit typical 'Variegata' symptoms, and steps were taken to identify any agents causing the 'off-type' symptoms. One of the viruses identified in the atypical 'Variegata' clone is a previously unknown virus, a member of the family Flexiviridae. Sequence and phylogenetic analysis indicate that the virus, designated as mint virus-2, is related to members of the species Grapevine virus A, Grapevine virus B and Heracleum latent virus, placing it in the genus Vitivirus. A detection protocol for the virus has been developed, and the mint aphid (Ovatus crataegarius) was able to transmit the virus in the presence of a helper virus but not from single infected plants.
Collapse
Affiliation(s)
- I E Tzanetakis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA.
| | | | | |
Collapse
|
28
|
Teycheney PY, Acina I, Lockhart BEL, Candresse T. Detection of Banana mild mosaic virus and Banana virus X by polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR). J Virol Methods 2007; 142:41-9. [PMID: 17280722 DOI: 10.1016/j.jviromet.2007.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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: 10/02/2006] [Revised: 12/22/2006] [Accepted: 01/11/2007] [Indexed: 11/23/2022]
Abstract
Viruses are important constraints to the movement and propagation of plant germplasm, especially for vegetatively propagated crops such as banana and plantain. Their control relies primarily on the use of virus-free plant material, whose production and certification requires sensitive and reliable detection methods. An existing polyvalent degenerate oligonucleotide RT-PCR (PDO-RT-PCR) assay was adapted to the detection of Banana mild mosaic virus (BanMMV) and Banana virus X, two Flexiviridae infecting Musa spp. PDO inosine-containing primers were found to be well suited to the detection of BanMMV, despite its high molecular diversity, but not to that of the highly conserved BVX, for which species-specific primers were designed. Sampling and sample processing steps were optimized in order to avoid nucleic acid purification prior to the reverse transcription step. A polyclonal anti-BanMMV antiserum was raised and successfully used for the immunocapture (IC) of BanMMV viral particles from leaf extracts, leading to the development of a PDO-IC-RT-nested PCR assay. Although the anti-BanMMV antiserum could to some extent recognize BVX viral particles, direct binding (DB) was shown to be a more efficient method for processing BVX-infected samples and a PDO-DB-RT-nested PCR assay was developed for the detection of BVX from leaf extracts.
Collapse
Affiliation(s)
- Pierre-Yves Teycheney
- CIRAD, UPR75, Station de Neufchâteau, F-97130 Capesterre Belle-Eau, FWI, Guadeloupe.
| | | | | | | |
Collapse
|
29
|
Prosser SW, Goszczynski DE, Meng B. Molecular analysis of double-stranded RNAs reveals complex infection of grapevines with multiple viruses. Virus Res 2006; 124:151-9. [PMID: 17129630 DOI: 10.1016/j.virusres.2006.10.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [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: 08/29/2006] [Revised: 10/26/2006] [Accepted: 10/27/2006] [Indexed: 11/28/2022]
Abstract
The table grape variety "Waltham Cross" was infected with Leafroll and Shiraz Disease. To reveal specific viruses that are associated with the diseased plants, we used an RT-PCR-based strategy to determine partial genome sequences of these viruses. Upon cloning and sequencing of the RT-PCR products, we detected seven groups of viral variants that are related to four species of the Closteroviridae: Grapevine leafroll-associated virus 1, 2, 3, and 5, in addition to Rupestris stem pitting-associated virus. The population composition of GLRaV-2 and GLRaV-3-like viruses is complex and consists of two or three distinct groups of viral variants. Based on the consensus sequence of several GLRaV-2 strains, we designed a pair of broad-spectrum primers (GLR2-4 and GLR2-5) and used them to detect a range of GLRaV-2 variants from "Waltham Cross". Moreover, we identified a novel group of viral variants from the diseased grapevines, which possess a stretch of 19 nucleotides inserted in the 3' non-coding region as compared to strain "PN" and "93/955" for which the complete genomes have been sequenced. In contrast, the population composition of GLRaV-1 and GLRaV-5-like virus seems to be more uniform and each consists of a single viral variant. Furthermore, the central 5.7kb genomic region encompassing ORF1b-ORF4 of the GLRaV-1 isolate detected in "Waltham Cross" was sequenced. The new isolate is designated GLRaV-1 "WC", which differs from GLRaV-1 "Type" by 16% in nucleotide sequence. The taxonomic standing of the GLRaV-5-like and GLRaV-3-like viruses detected in "Waltham Cross" is discussed.
Collapse
Affiliation(s)
- Sean W Prosser
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | | | | |
Collapse
|
30
|
Ma Y, Yang G, Xu S, Wei J, Qiu B. [Cloning and expression of two garlic virus coat protein genes]. Wei Sheng Wu Xue Bao 2001; 41:415-20. [PMID: 12552905] [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] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The coat protein(CP) genes of garlic mosaic virus(GMVc) and garlic latent virus(GLVc) isolated from garlic(Allium) plants in Tianjin, China, were amplified from an established cDNA library by PCR method and subsequently expressed in E. coli. using the pET-30a expression system. The determined sequences of GMVc and GLVc CP genes show that the complete GMVc CP gene has 867 nucleotides encoding 289 amino acids. It has 88.5% and 97.2% homology, at the levels of nucleotide and amino acid, respectively, to a reported GMV, indicating that it belongs to Potyvirus. The complete GLVc CP gene has 885 nucleotides coding for 294 amino acids. It has 73.6% and 90.9% homologous percents, in nucleotide and amino acid, respectively, compared to a previously reported GLV, suggesting that it is a member of Carlavirus. The expressed products presented in inclusion body and were analyzed by SDS-PAGE. The molecular weights of GMVc and GLVc CPs appear in 32 kD and 34 kD size, respectively, which are consistent with the deduced sizes of these two CPs. These data will be virtually significant to the further investigation of viruses infecting parlic plant, the control of garlic virus diseases and the production of virus-freed garlic plants.
Collapse
Affiliation(s)
- Y Ma
- Chemistry and Life College of Tianjin Teachers University, Tianjin 300074, China
| | | | | | | | | |
Collapse
|