1,029 results on '"Closterovirus"'
Search Results
2. Complete genome sequence of a novel closterovirus isolated from Dregea volubilis.
- Author
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Li, Shangyun, Anane, Rex Frimpong, Chen, Zeli, Duan, Chunfang, Wang, Zhe, Gao, Like, Yu, Daihong, Chu, Bifan, Yang, Zefen, Wen, Guosong, and Zhao, Mingfu
- Abstract
The complete genome sequence of a putative novel closterovirus, tentatively named "Dregea volubilis closterovirus 1" (DvCV1, GenBank accession no. MZ779122), infecting Dregea volubilis in China was determined using high-throughput sequencing (HTS). The complete genome sequence of DvCV1 consists of 16,165 nucleotides (nt) and contains nine ORFs. The genome structure of DvCV1 is typical of members of the genus Closterovirus. Complete genome sequence analysis showed that DvCV1 shares 41.4–48.4% nucleotide sequence identity with other known closteroviruses. The putative RNA-dependent RNA polymerase (RdRp), heat shock protein 70-like protein (HSP70h), and coat protein (CP) of DvCV1 share 46.80-62.65%, 31.06–51.80%, and 28.34–37.37% amino acid sequence identity, respectively, with the RdRp, HSP70h and CP of other closteroviruses. Phylogenetic analysis based on HSP70h aa sequences placed DvCV1 alongside other members of the genus Closterovirus in the family Closteroviridae. These results suggest that DvCV1 is a new member of the genus Closterovirus. This is the first report of a closterovirus infecting D. volubilis. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. A Chronological Study on Grapevine Leafroll-Associated Virus 2 in Australia.
- Author
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Habili, Nuredin, Wu, Qi, Rinaldo, Amy, and Constable, Fiona
- Subjects
- *
GRAPEVINE leafroll virus , *GRAPES , *VITIS vinifera , *CULTIVARS , *PLANT viruses - Abstract
Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological record of the temporal occurrence of GLRaV-2 in Australia since 2001 is reported. From a total of 11,257 samples, 313 tested positive, with an overall incidence of 2.7%. This virus has been detected in 18 grapevine varieties and Vitis rootstocks in different regions of Australia. Most varieties were symptomless on their own roots, while Chardonnay showed a decline in virus-sensitive rootstocks. An isolate of GLRaV-2, on own-rooted Vitis vinifera cv. Grenache, clone SA137, was associated with severe leafroll symptoms after veraison with abnormal leaf necrosis. The metagenomic sequencing results of the virus in two plants of this variety confirmed the presence of GLRaV-2, as well as two inert viruses, grapevine rupestris stem pitting-associated virus (GRSPaV) and grapevine rupestris vein feathering virus (GRVFV). No other leafroll-associated viruses were detected. Among the viroids, hop stunt viroid and grapevine yellow speckle viroid 1 were detected. Of the six phylogenetic groups identified in GLRaV-2, we report the presence of four groups in Australia. Three of these groups were detected in two plants of cv. Grenache, without finding any recombination event. The hypersensitive reaction of certain American hybrid rootstocks to GLRaV-2 is discussed. Due to the association of GLRaV-2 with graft incompatibility and vine decline, the risk from this virus in regions where hybrid Vitis rootstocks are used cannot be overlooked. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
4. Transcriptomic alterations in the sweet orange vasculature correlate with growth repression induced by a variant of citrus tristeza virus.
- Author
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Aknadibossian, Vicken, Huguet-Tapia, Jose C., Golyaev, Victor, Pooggin, Mikhail M., and Folimonova, Svetlana Y.
- Subjects
CITRUS tristeza virus ,SMALL interfering RNA ,CYSTEINE proteinases ,TRANSCRIPTOMES ,ORANGES ,HEAT shock proteins - Abstract
Citrus tristeza virus (CTV, family Closteroviridae) is an economically important pathogen of citrus. CTV resides in the phloem of the infected plants and induces a range of disease phenotypes, including stem pitting and quick decline as well as a number of other deleterious syndromes. To uncover the biological processes underlying the poorly understood damaging symptoms of CTV, we profiled the transcriptome of sweet orange (Citrus sinensis) phloem-rich bark tissues of non-infected, mock-inoculated trees and trees singly infected with two distinct variants of CTV, T36 or T68-1. The T36 and T68-1 variants accumulated in the infected plants at similar titers. With that, young trees infected with T68-1 were markedly repressed in growth, while the growth rate of the trees infected with T36 was comparable to the mock-inoculated trees. Only a small number of differentially expressed genes (DEGs) were identified in the nearly asymptomatic T36-infected trees, whereas almost fourfold the number of DEGs were identified with the growth-restricting T68-1 infection. DEGs were validated using quantitative reverse transcription-PCR. While T36 did not induce many noteworthy changes, T68-1 altered the expression of numerous host mRNAs encoding proteins within significant biological pathways, including immunity and stress response proteins, papain-like cysteine proteases (PLCPs), cell-wall modifying enzymes, vascular development proteins and others. The transcriptomic alterations in the T68-1- infected trees, in particular, the strong and persistent increase in the expression levels of PLCPs, appear to contribute to the observed stem growth repression. On the other hand, analysis of the viral small interfering RNAs revealed that the host RNA silencing-based response to the infection by T36 and that by T68-1 was comparable, and thus, the induction of this antiviral mechanism may not contribute to the difference in the observed symptoms. The DEGs identified in this study promote our understanding of the underlying mechanisms of the yet unexplained growth repression induced by severe CTV isolates in sweet orange trees. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan.
- Author
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Kondo, Hideki, Sugahara, Hitomi, Fujita, Miki, Hyodo, Kiwamu, Andika, Ida Bagus, Hisano, Hiroshi, and Suzuki, Nobuhiro
- Subjects
BARLEY yellow dwarf viruses ,MOSAIC viruses ,WINTER wheat ,WHEAT ,RHOPALOSIPHUM padi ,FOLIAGE plants ,NON-coding RNA ,VIRAL genomes - Abstract
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the field have not been investigated. We observed yellowing leaves in the 2018/2019 winter wheat-growing season in an experimental field in Japan where WYLV was detected five decades ago. A virome analysis of those yellow leaf samples lead to the discovery of a closterovirus together with a luteovirus (barley yellow dwarf virus PAV variant IIIa). The complete genomic sequence of this closterovirus, named wheat closterovirus 1 isolate WL19a (WhCV1-WL19a), consisted of 15,452 nucleotides harboring nine open reading frames. Additionally, we identified another WhCV1 isolate, WL20, in a wheat sample from the winter wheat-growing season of 2019/2020. A transmission test indicated that WhCV1-WL20 was able to form typical filamentous particles and transmissible by oat bird-cherry aphid (Rhopalosiphum pad). Sequence and phylogenetic analyses showed that WhCV1 was distantly related to members of the genus Closterovirus (family Closteroviridae), suggesting that the virus represents a novel species in the genus. Furthermore, the characterization of WhCV1-WL19a-derived small RNAs using high-throughput sequencing revealed highly abundant 22-nt-class small RNAs potentially derived from the 3′-terminal end of the WhCV1 negative-strand genomic RNA, indicating that this terminal end of the WhCV1 genome is likely particularly targeted for the synthesis of viral small RNAs in wheat plants. Our results provide further knowledge on closterovirus diversity and pathogenicity and suggest that the impact of WhCV1 on wheat production warrants further investigations. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
6. Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host.
- Author
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Biswas, Kajal, Palchoudhury, Supratik, Chakraborty, Prosenjit, Bhattacharyya, Utpal, Ghosh, Dilip, Debnath, Palash, Ramadugu, Chandrika, Keremane, Manjunath, Khetarpal, Ravi, and Lee, Richard
- Subjects
Citrus tristeza virus ,citrus host ,codon usage adaptation ,codon usage bias ,high-frequency codons ,natural selection ,Adaptation ,Biological ,Capsid Proteins ,Citrus ,Citrus aurantiifolia ,Citrus sinensis ,Closterovirus ,Codon Usage ,Genomic Instability ,RNA ,Viral - Abstract
Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host⁻virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.
- Published
- 2019
7. Transcriptomic alterations in the sweet orange vasculature correlate with growth repression induced by a variant of citrus tristeza virus
- Author
-
Vicken Aknadibossian, Jose C. Huguet-Tapia, Victor Golyaev, Mikhail M. Pooggin, and Svetlana Y. Folimonova
- Subjects
RNA virus ,closterovirus ,citrus tristeza virus ,plant virus ,transcriptome ,small RNA ,Microbiology ,QR1-502 - Abstract
Citrus tristeza virus (CTV, family Closteroviridae) is an economically important pathogen of citrus. CTV resides in the phloem of the infected plants and induces a range of disease phenotypes, including stem pitting and quick decline as well as a number of other deleterious syndromes. To uncover the biological processes underlying the poorly understood damaging symptoms of CTV, we profiled the transcriptome of sweet orange (Citrus sinensis) phloem-rich bark tissues of non-infected, mock-inoculated trees and trees singly infected with two distinct variants of CTV, T36 or T68-1. The T36 and T68-1 variants accumulated in the infected plants at similar titers. With that, young trees infected with T68-1 were markedly repressed in growth, while the growth rate of the trees infected with T36 was comparable to the mock-inoculated trees. Only a small number of differentially expressed genes (DEGs) were identified in the nearly asymptomatic T36-infected trees, whereas almost fourfold the number of DEGs were identified with the growth-restricting T68-1 infection. DEGs were validated using quantitative reverse transcription-PCR. While T36 did not induce many noteworthy changes, T68-1 altered the expression of numerous host mRNAs encoding proteins within significant biological pathways, including immunity and stress response proteins, papain-like cysteine proteases (PLCPs), cell-wall modifying enzymes, vascular development proteins and others. The transcriptomic alterations in the T68-1-infected trees, in particular, the strong and persistent increase in the expression levels of PLCPs, appear to contribute to the observed stem growth repression. On the other hand, analysis of the viral small interfering RNAs revealed that the host RNA silencing-based response to the infection by T36 and that by T68-1 was comparable, and thus, the induction of this antiviral mechanism may not contribute to the difference in the observed symptoms. The DEGs identified in this study promote our understanding of the underlying mechanisms of the yet unexplained growth repression induced by severe CTV isolates in sweet orange trees.
- Published
- 2023
- Full Text
- View/download PDF
8. Two Crinivirus-Conserved Small Proteins, P5 and P9, Are Indispensable for Efficient Lettuce infectious yellows virus Infectivity in Plants.
- Author
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Qiao, Wenjie, Helpio, Erin L, and Falk, Bryce W
- Subjects
Endoplasmic Reticulum ,Closterovirus ,Crinivirus ,Lettuce ,Tobacco ,Plant Leaves ,Viral Proteins ,RNA ,Viral ,Cell Death ,Plant Diseases ,Amino Acid Sequence ,Mutation ,Genome ,Viral ,Open Reading Frames ,Gene Knockout Techniques ,Unfolded Protein Response ,ER stress ,Lettuce infectious yellows virus ,P5 ,P9 ,small ORFs ,virus infectivity ,RNA ,Viral ,Genome ,Microbiology - Abstract
Genomic analysis of Lettuce infectious yellows virus (LIYV) has revealed two short open reading frames (ORFs) on LIYV RNA2, that are predicted to encode a 5-kDa (P5) and a 9-kDa (P9) protein. The P5 ORF is part of the conserved quintuple gene block in the family Closteroviridae, while P9 orthologs are found in all Criniviruses. In this study, the expression of LIYV P5 and P9 proteins was confirmed; P5 is further characterized as an endoplasmic reticulum (ER)-localized integral transmembrane protein and P9 is a soluble protein. The knockout LIYV mutants presented reduced symptom severity and virus accumulation in Nicotiana benthamiana or lettuce plants, indicating their importance in efficient virus infection. The P5 mutant was successfully complemented by a dislocated P5 in the LIYV genome. The structural regions of P5 were tested and all were found to be required for the appropriate functions of P5. In addition, P5, as well as its ortholog P6, encoded by Citrus tristeza virus (CTV) and another ER-localized protein encoded by LIYV RNA1, were found to cause cell death when expressed in N. benthamiana plants from a TMV vector, and induce ER stress and the unfolded protein response (UPR).
- Published
- 2018
9. Virus Yellows and Syndrome "Basses Richesses" in Western Switzerland: A Dramatic 2020 Season Calls for Urgent Control Measures.
- Author
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Mahillon, Mathieu, Groux, Raphaël, Bussereau, Floriane, Brodard, Justine, Debonneville, Christophe, Demal, Sonia, Kellenberger, Isabelle, Peter, Madlaina, Steinger, Thomas, and Schumpp, Olivier
- Subjects
BARLEY yellow dwarf viruses ,PHYTOPLASMAS ,MOSAIC viruses ,RNA viruses ,NUCLEOTIDE sequencing - Abstract
Massive outbreaks of virus yellows (VY) and syndrome "basses richesses" (SBR) are thought to be responsible for the major loss of sugar beet yields in 2020 in western cantons of Switzerland. Typical yellowing symptoms were visible during field inspections, and control measures were reportedly ineffective or even absent. Both diseases induce yellowing but have distinct etiologies; while VY is caused by aphid-transmitted RNA viruses, SBR is caused by the cixiid-transmitted γ-proteobacterium Candidatus Arsenophonus phytopathogenicus. To clarify the situation, samples from diseased plants across the country were screened for the causal agents of VY and SBR at the end of the season. Beet yellows virus (BYV) and Beet chlorosis virus (BChV) showed high incidence nationwide, and were frequently found together in SBR-infected fields in the West. Beet mild yellowing virus (BMYV) was detected in two sites in the West, while there was no detection of Beet western yellows virus or Beet mosaic virus. The nucleotide diversity of the detected viruses was then investigated using classic and high-throughput sequencing. For both diseases, outbreaks were analyzed in light of monitoring of the respective vectors, and symptoms were reproduced in greenhouse conditions by means of insect-mediated inoculations. Novel quantification tools were designed for BYV, BChV and Ca. A. phytopathogenicus, leading to the identification of specific tissues tropism for these pathogens. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
10. A novel RNA virus, Thesium chinense closterovirus 1, identified by high-throughput RNA-sequencing of the parasitic plant Thesium chinense.
- Author
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Chaerim Shin, Dongjin Choi, Ken Shirasu, Yasunori Ichihashi, and Yoonsoo Hahn
- Subjects
PARASITIC plants ,RNA sequencing ,HEAT shock proteins ,RNA replicase ,RNA viruses ,PEPPERS - Abstract
The genome sequence of a closterovirus (genus Closterovirus, family Closteroviridae), tentatively named Thesium chinense closterovirus 1 (TcCV1), was identified by performing high-throughput RNA-sequencing of the haustoria and root tissues of Thesium chinense, a parasitic plant. The TcCV1 genome was predicted to encode nine proteins, eight of which have orthologs in previously identified closteroviruses. The TcCV1 RNA-dependent RNA polymerase (RdRp) and heat shock protein 70 homolog (Hsp70h) showed 27.8–68.2% and 23.8–55.1% amino acid identity, respectively, to orthologous proteins of known closteroviruses. The putative +1 ribosomal frameshifting site required for producing RdRp was identified as GUUUAGC with UAG stop codon and the skipped nucleotide U. Phylogenetic trees based on RdRp and Hsp70h show that TcCV1 is a novel member of the genus Closterovirus, forming a subclade with a group of known closteroviruses, including mint virus 1 and carnation necrotic fleck virus. The genome sequence of TcCV1 may be useful for studying the genome evolution of closteroviruses. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
11. A Chronological Study on Grapevine Leafroll-Associated Virus 2 in Australia
- Author
-
Nuredin Habili, Qi Wu, Amy Rinaldo, and Fiona Constable
- Subjects
grapevine leafroll-associated virus 2 ,Closterovirus ,graft incompatibility ,hypersensitive reaction ,RNA silencing suppressor ,Microbiology ,QR1-502 - Abstract
Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological record of the temporal occurrence of GLRaV-2 in Australia since 2001 is reported. From a total of 11,257 samples, 313 tested positive, with an overall incidence of 2.7%. This virus has been detected in 18 grapevine varieties and Vitis rootstocks in different regions of Australia. Most varieties were symptomless on their own roots, while Chardonnay showed a decline in virus-sensitive rootstocks. An isolate of GLRaV-2, on own-rooted Vitis vinifera cv. Grenache, clone SA137, was associated with severe leafroll symptoms after veraison with abnormal leaf necrosis. The metagenomic sequencing results of the virus in two plants of this variety confirmed the presence of GLRaV-2, as well as two inert viruses, grapevine rupestris stem pitting-associated virus (GRSPaV) and grapevine rupestris vein feathering virus (GRVFV). No other leafroll-associated viruses were detected. Among the viroids, hop stunt viroid and grapevine yellow speckle viroid 1 were detected. Of the six phylogenetic groups identified in GLRaV-2, we report the presence of four groups in Australia. Three of these groups were detected in two plants of cv. Grenache, without finding any recombination event. The hypersensitive reaction of certain American hybrid rootstocks to GLRaV-2 is discussed. Due to the association of GLRaV-2 with graft incompatibility and vine decline, the risk from this virus in regions where hybrid Vitis rootstocks are used cannot be overlooked.
- Published
- 2023
- Full Text
- View/download PDF
12. Dwarf polish wheat hosts a novel closterovirus: Revelation by transcriptome data-mining.
- Author
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Sidharthan, Venkidusamy Kavi and Baranwal, Virendra Kumar
- Subjects
TRANSCRIPTOMES ,DATA mining ,PLANT RNA ,PLANT viruses ,VIRAL replication - Abstract
Closteroviruses are positive sense single-stranded RNA genome-containing plant viruses with narrow natural host range and wide distribution. In the present study, a putative novel closterovirus, Triticum polonicum closterovirus (TriPCV) was identified in the transcriptome assembled contigs of dwarf polish wheat available in public domain. The genome of TriPCV (15.36 kb; TPA Acc. No.: BK059767) contained nine open reading frames (ORFs) that encode for proteins involved in viral replication, cell-tocell movement, encapsidation and suppression of host RNA silencing. Phylogenetic analysis revealed that TriPCV was distantly related to other members of the genus Closterovirus. Based on genome organization, sequence similarities in BLAST analysis, predicted motifs and phylogeny, TriPCV can be regarded as a putative novel member of the genus Closterovirus. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
13. Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan
- Author
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Hideki Kondo, Hitomi Sugahara, Miki Fujita, Kiwamu Hyodo, Ida Bagus Andika, Hiroshi Hisano, and Nobuhiro Suzuki
- Subjects
wheat ,closterovirus ,yellow leaf disease ,RNA-seq ,aphid transmission ,RNA silencing ,Medicine - Abstract
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the field have not been investigated. We observed yellowing leaves in the 2018/2019 winter wheat-growing season in an experimental field in Japan where WYLV was detected five decades ago. A virome analysis of those yellow leaf samples lead to the discovery of a closterovirus together with a luteovirus (barley yellow dwarf virus PAV variant IIIa). The complete genomic sequence of this closterovirus, named wheat closterovirus 1 isolate WL19a (WhCV1-WL19a), consisted of 15,452 nucleotides harboring nine open reading frames. Additionally, we identified another WhCV1 isolate, WL20, in a wheat sample from the winter wheat-growing season of 2019/2020. A transmission test indicated that WhCV1-WL20 was able to form typical filamentous particles and transmissible by oat bird-cherry aphid (Rhopalosiphum pad). Sequence and phylogenetic analyses showed that WhCV1 was distantly related to members of the genus Closterovirus (family Closteroviridae), suggesting that the virus represents a novel species in the genus. Furthermore, the characterization of WhCV1-WL19a-derived small RNAs using high-throughput sequencing revealed highly abundant 22-nt-class small RNAs potentially derived from the 3′-terminal end of the WhCV1 negative-strand genomic RNA, indicating that this terminal end of the WhCV1 genome is likely particularly targeted for the synthesis of viral small RNAs in wheat plants. Our results provide further knowledge on closterovirus diversity and pathogenicity and suggest that the impact of WhCV1 on wheat production warrants further investigations.
- Published
- 2023
- Full Text
- View/download PDF
14. Grapevine leafroll-associated virus 2
- Author
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Angelini, E., Aboughanem-Sabanadzovic, N., Dolja, V. V., Meng, B., Meng, Baozhong, editor, Martelli, Giovanni P., editor, Golino, Deborah A., editor, and Fuchs, Marc, editor
- Published
- 2017
- Full Text
- View/download PDF
15. Two novel closteroviruses, fig virus A and fig virus B, identified by the analysis of the high-throughput RNA-sequencing data of fig (Ficus carica) latex.
- Author
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Park, Dongbin, Chul Jun Goh, and Yoonsoo Hahn
- Subjects
CLOSTEROVIRUSES ,FIG ,RNA viruses ,VIRUS diseases of plants ,PLANT viruses - Abstract
Closteroviruses (the genus Closterovirus, the family Closteroviridae) are RNA viruses that infect and cause viral diseases in many economically important plants. Genome sequences of two novel closteroviruses named fig virus A (FiVA) and fig virus B (FiVB) were identified in high-throughput sequencing data obtained from a fig latex sample. FiVA and FiVB genomes, whose lengths are 19,333 bp and 18,741 bp, respectively, were predicted to have 14 shared open reading frames, nine of which had homologs in other closteroviruses. Phylogenetic analysis confirmed that FiVA and FiVB are novel closteroviruses forming a strong subclade with fig mild mottle-associated virus within the genus Closterovirus. FiVA and FiVB genome sequences identified in this study are useful resources for investigating the evolution of closterovirus genome organization. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
16. PCR cuantitativa para la detección del virus de la tristeza de los cítricos en Colombia
- Author
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Luis Miguel Solano-Luna, Edisson Chavarro-Mesa, and Jorge Evelio Ángel-Diaz
- Subjects
Closterovirus ,cuantificación absoluta ,detección de patógenos vegetales ,enfermedades de los cítricos ,PCR en tiempo real SYBR Green ,Agriculture ,Agriculture (General) ,S1-972 - Abstract
Se aplicó la técnica de reacción en cadena de la polimerasa en tiempo real (qRT-PCR), usando SYBR Green para la detección específica del virus de la tristeza de los cítricos (CTV) en Colombia. Una pareja de iniciadores, diseñados a partir de secuencias conservadas en los marcos abiertos de lectura (ORF’s) 1b y 2, permitió amplificar el ARN genómico (ARNg), y un producto de 186 pb fue obtenido sin la presencia de dímeros o inespecificidad. El análisis de la curva de fusión mostró un pico entre 81 oC y 83 oC, con un coeficiente de correlación de 0,998 y una eficiencia de 99,1 %. La curva estándar se desarrolló a partir de una amplificación del producto de 186 pb y permitió realizar un análisis cuantitativo de las muestras, con un rango de detección de 1x108 hasta 1x103 copias de RNAg y con valores de coeficiente de variación bajos. La acumulación de CTV fue más alta en tejido foliar y en frutos que en corteza; entretanto, las diferencias demostradas entre varias especies de cítricos susceptibles a la infección fueron mínimas. Los resultados de este trabajo muestran que la mayor concentración de virus se encontró en el tercio superior de las plantas analizadas, seguida por el tercio bajo y, por último, el tercio medio. La qRT-PCR es un método específico y sensible de interés práctico en los procesos de detección de las enfermedades virales presentes en el cultivo de los cítricos y otros cultivos de interés comercial.
- Published
- 2018
- Full Text
- View/download PDF
17. The Intriguing Conundrum of a Nonconserved Multifunctional Protein of Citrus Tristeza Virus That Interacts with a Viral Long Non-Coding RNA
- Author
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Sung-Hwan Kang, Vicken Aknadibossian, Laxmi Kharel, Shachinthaka D. Dissanayaka Mudiyanselage, Ying Wang, and Svetlana Y. Folimonova
- Subjects
RNA virus ,closterovirus ,citrus tristeza virus ,long non-coding RNA ,plant virus ,RNA-binding protein ,Microbiology ,QR1-502 - Abstract
Citrus tristeza virus (CTV), the largest non-segmented plant RNA virus, has several peculiar features, among which is the production of a 5′-terminal long non-coding RNA (lncRNA) termed low-molecular-weight tristeza 1 (LMT1). In this study, we found that p33, a unique viral protein that performs multiple functions in the virus infection cycle, specifically binds LMT1, both in vivo and in vitro. These results were obtained through the expression of p33 under the context of the wild type virus infection or along with a mutant CTV variant that does not produce LMT1 as well as via ectopic co-expression of p33 with LMT1 in Nicotiana benthamiana leaves followed by RNA immunoprecipitation and rapid amplification of cDNA ends assays. Further experiments in which a recombinant p33 protein and an in vitro transcribed full-length LMT1 RNA or its truncated fragments were subjected to an electrophoretic mobility shift assay demonstrated that p33 binds to at least two distinct regions within LMT1. To the best of our knowledge, this is the first report of a plant virus protein binding to a lncRNA produced by the same virus. The biological significance of the interaction between these two viral factors is discussed.
- Published
- 2021
- Full Text
- View/download PDF
18. First report of citrus tristeza virus in Lao PDR.
- Author
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Donovan, N. J., Englezou, A., Chambers, G. A., Phanthavong, S., Daly, A., Saleh, F., Holford, P., and Burgess, L. W.
- Abstract
Citrus tristeza virus was detected for the first time in the Lao People's Democratic Republic. Samples were collected from citrus trees across the southern provinces for testing in Australia. RNA was extracted and tested using conventional and real-time reverse transcription polymerase chain reactions with the virus detected in 12 of 59 samples tested. Viral identities were confirmed by sequencing. Additional confirmation was obtained by an enzyme-linked immunosorbent assay. The implications of the presence of this virus for citrus production in Lao are discussed briefly. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
19. Molecular studies on cucurbit yellow stunting disorder virus
- Author
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Livieratos, Ioannis
- Subjects
579 ,Cucumber ,Disease ,CYSDV ,Closterovirus ,Whitefly - Published
- 1999
20. Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
- Author
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Hanna Susi, Denis Filloux, Mikko J. Frilander, Philippe Roumagnac, and Anna-Liisa Laine
- Subjects
Betapartitivirus ,Caulimovirus ,Closterovirus ,Metagenomics ,Enamovirus ,Plantago lanceolata latent virus ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
- Published
- 2019
- Full Text
- View/download PDF
21. Report of Citrus tristeza virus in Diaphorina citri (Hemiotera: Liviidae) insects of different sexes, color morphs, and developmental stages.
- Author
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Zhang J, Xiao Y, Hu P, Chen L, Deng X, and Xu M
- Subjects
- Animals, Plant Diseases, Nymph, Hemiptera, Rhizobiaceae, Citrus, Aphids, Liberibacter, Closterovirus
- Abstract
Diaphorina citri, also known as the Asian citrus psyllid, is the main vector of 'Candidatus Liberibacter asiaticus' (CLas) associated with citrus Huanglongbing. It has been reported that D. citri could also be infected by Citrus tristeza virus (CTV), a virus that has been previously reported to be vectored by certain aphid species. In this study, the CTV and CLas profiles in different organs, color variants, developmental stages, or sexes of D. citri insects were analyzed. Although no significant differences were found between nymphs and adults in CTV titers, we found that the third instar nymph of D. citri was more efficient in CTV and CLas acquisition compared to the fourth and fifth instars and adults. With the instars of D. citri development, the relationship between the acquiring of CTV and CLas by D. citri seemed to follow an inverse trend, with the titer of CLas increased and the titer of CTV decreased. No significant differences were observed between the 2 sexes of D. citri in acquiring either CTV or CLas titers in the field. However, no differences were drawn among the 3 color morph variants for CTV titers. CTV titers in the midguts of adult D. citri were significantly higher than those in the salivary glands. Both CTV-positive incidence and CTV titers in the midguts of adult D. citri increased with increasing exposure periods. This study provides new data to deepen our understanding of the CTV-involved interaction between D. citri and CLas., (© The Author(s) 2024. Published by Oxford University Press on behalf of Entomological Society of America.)
- Published
- 2024
- Full Text
- View/download PDF
22. Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes
- Author
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Yashu Song, Robert H. Hanner, and Baozhong Meng
- Subjects
grapevine ,grapevine leafroll disease ,grapevine leafroll-associated viruses ,Ampelovirus ,Closterovirus ,Velarivirus ,Microbiology ,QR1-502 - Abstract
Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops.
- Published
- 2021
- Full Text
- View/download PDF
23. Bottom-up regulation of a tritrophic system by Beet yellows virus infection: consequences for aphid-parasitoid foraging behaviour and development.
- Author
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Albittar, Loulou, Ismail, Mohannad, Lohaus, Gertrud, Ameline, Arnaud, Visser, Bertanne, Bragard, Claude, and Hance, Thierry
- Subjects
- *
VIRUS diseases , *PHYTOPLASMAS , *FOOD chains , *PLANT viruses , *BEETS , *FORAGE plants , *BIOLOGICAL pest control , *PARASITISM - Abstract
Effects of plants on herbivores can cascade up the food web and modulate the abundance of higher trophic levels. In agro-ecosystems, plant viruses can affect the interactions between crops, crop pests, and natural enemies. Little is known, however, about the effects of viruses on higher trophic levels, including parasitoids and their ability for pest regulation. We tested the hypothesis that a plant virus affects parasitoid foraging behaviour through cascading effects on higher trophic levels. We predicted that the semi-persistent Beet yellows virus (BYV) would influence plant (Beta vulgaris) quality, as well as aphid host (Aphis fabae) quality for a parasitoid Lysiphlebus fabarum. We determined amino acid and sugar content in healthy and infected plants (first trophic level), lipid content and body size of aphids (second trophic level) fed on both plants, as well as foraging behaviour and body size of parasitoids (third trophic level) that developed on aphids fed on both plants. Our results showed that virus infection increased sugars and decreased total amino acid content in B. vulgaris. We further observed an increase in aphid size without modification in host aphid quality (i.e., lipid content), and a slight effect on parasitoid behaviour through an increased number of antennal contacts with host aphids. Although the BYV virus clearly affected the first two trophic levels, it did not affect development or emergence of parasitoids. As the parasitoid L. fabarum does not seem to be affected by the virus, we discuss the possibility of using it for the development of targeted biological control against aphids. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
24. Biological and molecular characterization of Uruguayan citrus tristeza virus field isolates.
- Author
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Rubio, Leticia, Bertalmío, Ana, Hernández-Rodríguez, Lester, Benítez Galeano, María José, Arruabarrena, Ana, Rivas, Fernando, Colina, Rodney, and Maeso, Diego
- Subjects
CITRUS tristeza virus ,CITRUS diseases & pests ,ROOTSTOCKS ,DISEASE resistance of plants ,ORCHARDS ,POLYMERASE chain reaction ,NUCLEOTIDE sequence - Abstract
Citrus tristeza virus (CTV) is the causal agent of the most important viral disease of citrus. Symptoms that may affect the productive potential of citrus plants are observed in Uruguayan orchards even though resistant rootstocks are used. CTV is fully eliminated in propagative materials by the National Sanitation and Certification Program, but since the virus and its vector are widespread in the country, the risk of infection in the field persists. In this situation, using mild CTV strains in a cross-protection program would be a useful alternative to attempt to increase yield and quality of the local citrus industry. To this aim, this study assessed the biological and molecular characteristics of 32 local CTV isolates. Bioassays were conducted in a greenhouse with controlled conditions. Each isolate was graft-inoculated on Mexican lime, sweet orange, sour orange and Duncan grapefruit indicator plants. Symptoms and their intensity were evaluated. Molecular characterization was carried out by RT-PCR amplification, using primers for the p25, p20 and p23 genes. PCR products were sequenced, nucleotide sequences were aligned with international reference strains and phylogenetic trees were constructed. Results of the biological and molecular analysis showed the prevalence of severe CTV isolates with a high genetic variability. Two out of 32 characterized isolates were selected as mild CTV isolates to be tested as candidates for future cross-protection experiments. The survey showed a complex scenario for the management of CTV in Uruguay. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
25. Diverse and variable virus communities in wild plant populations revealed by metagenomic tools.
- Author
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Susi, Hanna, Filloux, Denis, Frilander, Mikko J., Roumagnac, Philippe, and Laine, Anna-Liisa
- Subjects
PLANT populations ,PLANT communities ,WILD plants ,PLANT viruses ,VIRUS diseases ,COEXISTENCE of species - Abstract
Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the ecoevolutionary dynamics of viruses infecting plants in the wild. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
26. GLRaV-2 protein p24 suppresses host defenses by interaction with a RAV transcription factor from grapevine
- Author
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Chenwei Zhang, Xianyou Wang, Hanwei Li, Jinying Wang, Qi Zeng, Wenting Huang, Haoqiang Huang, Yinshuai Xie, Shangzhen Yu, Qing Kan, Qi Wang, and Yuqin Cheng
- Subjects
Viral Proteins ,Closterovirus ,Physiology ,Genetics ,RNA Interference ,Vitis ,Plant Science ,Research Articles ,Plant Diseases ,Transcription Factors - Abstract
Grapevine leafroll-associated virus 2 (GLRaV-2) is a prevalent virus associated with grapevine leafroll disease, but the molecular mechanism underlying GLRaV-2 infection is largely unclear. Here, we report that 24-kDa protein (p24), an RNA-silencing suppressor (RSS) encoded by GLRaV-2, promotes GLRaV-2 accumulation via interaction with the B3 DNA-binding domain of grapevine (Vitis vinifera) RELATED TO ABSCISIC ACID INSENSITIVE3/VIVIPAROUS1 (VvRAV1), a transcription factor belonging to the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) superfamily. Salicylic acid-inducible VvRAV1 positively regulates the grapevine pathogenesis-related protein 1 (VvPR1) gene by directly binding its promoter, indicating that VvRAV1 may function in the regulation of host basal defense responses. p24 hijacks VvRAV1 to the cytoplasm and employs the protein to sequester 21-nt double-stranded siRNA together, thereby enhancing its own RSS activity. Moreover, p24 enters the nucleus via interaction with VvRAV1 and weakens the latter’s binding affinity to the VvPR1 promoter, leading to decreased expression of VvPR1. Our results provide a mechanism by which a viral RSS interferes with both the antiviral RNA silencing and the AP2/ERF-mediated defense responses via the targeting of one specific host factor.
- Published
- 2022
27. Semipersistently Transmitted, Phloem Limited Plant Viruses Are Inoculated during the First Subphase of Intracellular Stylet Penetrations in Phloem Cells
- Author
-
Jaime Jiménez, Aránzazu Moreno, and Alberto Fereres
- Subjects
Beet yellows virus ,Myzus persicae ,Closterovirus ,phloem-pd ,electrical penetration graphs ,Microbiology ,QR1-502 - Abstract
The green peach aphid Myzus persicae Sulzer is the main vector of the semipersistently transmitted and phloem-limited Beet yellows virus (BYV, Closterovirus). Studies monitoring the M. persicae probing behavior by using the Electrical penetration graphs (EPG) technique revealed that inoculation of BYV occurs during unique brief intracellular punctures (phloem-pds) produced in companion and/or sieve element cells. Intracellular stylet punctures (or pds) are subdivided in three subphases (II-1, II-2 and II-3), which have been related to the delivery or uptake of non-phloem limited viruses transmitted in a non-persistent or semipersistent manner. As opposed to non-phloem limited viruses, the specific pd subphase(s) involved in the successful delivery of phloem limited viruses by aphids remain unknown. Therefore, we monitored the feeding process of BYV-carrying M. persicae individuals in sugar beet plants by the EPG technique and the feeding process was artificially terminated at each phloem-pd subphase. Results revealed that aphids that only performed the subphase II-1 of the phloem-pd transmitted BYV at similar efficiency than those allowed to perform subphase II-2 or the complete phloem-pd. This result suggests that BYV inoculation occurs during the first subphase of the phloem-pd. The specific transmission mechanisms involved in BYV delivery in phloem cells are discussed.
- Published
- 2021
- Full Text
- View/download PDF
28. Walking Together: Cross-Protection, Genome Conservation, and the Replication Machinery of Citrus tristeza virus
- Author
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Svetlana Y. Folimonova, Diann Achor, and Moshe Bar-Joseph
- Subjects
RNA virus ,closterovirus ,Citrus tristeza virus ,cross-protection ,close protection ,superinfection exclusion ,Microbiology ,QR1-502 - Abstract
“Cross-protection”, a nearly 100 years-old virological term, is suggested to be changed to “close protection”. Evidence for the need of such change has accumulated over the past six decades from the laboratory experiments and field tests conducted by plant pathologists and plant virologists working with different plant viruses, and, in particular, from research on Citrus tristeza virus (CTV). A direct confirmation of such close protection came with the finding that “pre-immunization” of citrus plants with the variants of the T36 strain of CTV but not with variants of other virus strains was providing protection against a fluorescent protein-tagged T36-based recombinant virus variant. Under natural conditions close protection is functional and is closely associated both with the conservation of the CTV genome sequence and prevention of superinfection by closely similar isolates. It is suggested that the mechanism is primarily directed to prevent the danger of virus population collapse that could be expected to result through quasispecies divergence of large RNA genomes of the CTV variants continuously replicating within long-living and highly voluminous fruit trees. This review article provides an overview of the CTV cross-protection research, along with a discussion of the phenomenon in the context of the CTV biology and genetics.
- Published
- 2020
- Full Text
- View/download PDF
29. RNAi-Mediated Protection Against Citrus Tristeza Virus in Transgenic Citrus Plants
- Author
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Soler, Nuria, Fagoaga, Carmen, Chiibi, Sinda, López, Carmelo, Moreno, Pedro, Navarro, Luis, Flores, Ricardo, Peña, Leandro, Erdmann, Volker A., editor, and Barciszewski, Jan, editor
- Published
- 2011
- Full Text
- View/download PDF
30. Co-infection of Sweet Orange with Severe and Mild Strains of Citrus tristeza virus Is Overwhelmingly Dominated by the Severe Strain on Both the Transcriptional and Biological Levels
- Author
-
Shimin Fu, Jonathan Shao, Changyong Zhou, and John S. Hartung
- Subjects
Citrus sinensis ,transcriptome ,host–pathogen interaction ,defense response ,closterovirus ,Plant culture ,SB1-1110 - Abstract
Citrus tristeza is one of the most destructive citrus diseases and is caused by the phloem-restricted Closterovirus, Citrus tristeza virus. Mild strain CTV-B2 does not cause obvious symptoms on indicators whereas severe strain CTV-B6 causes symptoms, including stem pitting, cupping, yellowing, and stiffening of leaves, and vein corking. Our laboratory has previously characterized changes in transcription in sweet orange separately infected with CTV-B2 and CTV-B6. In the present study, transcriptome analysis of Citrus sinensis in response to double infection by CTV-B2 and CTV-B6 was carried out. Four hundred and eleven transcripts were up-regulated and 356 transcripts were down-regulated prior to the onset of symptoms. Repressed genes were overwhelmingly associated with photosynthesis, and carbon and nucleic acid metabolism. Expression of genes related to the glycolytic, oxidative pentose phosphate (OPP), tricarboxylic acid cycle (TCA) pathways, tetrapyrrole synthesis, redox homeostasis, nucleotide metabolism, protein synthesis and post translational protein modification and folding, and cell organization were all reduced. Ribosomal composition was also greatly altered in response to infection by CTV-B2/CTV-B6. Genes that were induced were related to cell wall structure, secondary and hormone metabolism, responses to biotic stress, regulation of transcription, signaling, and secondary metabolism. Transport systems dedicated to metal ions were especially disturbed and ZIPs (Zinc Transporter Precursors) showed different expression patterns in response to co-infection by CTV-B2/CTV-B6 and single infection by CTV-B2. Host plants experienced root decline that may have contributed to Zn, Fe, and other nutrient deficiencies. Though defense responses, such as, strengthening of the cell wall, alteration of hormone metabolism, secondary metabolites, and signaling pathways, were activated, these defense responses did not suppress the spread of the pathogens and the development of symptoms. The mild strain CTV-B2 did not provide a useful level of cross-protection to citrus against the severe strain CTV-B6.
- Published
- 2017
- Full Text
- View/download PDF
31. Molecular characterization of the 3′ end of Citrus tristeza virus genome from Oman
- Author
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Hanu R. Pappu, Muhammad Shahid, and Abdullah M. Al-Sadi
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,biology ,Phylogenetic tree ,Sequence analysis ,Citrus tristeza virus ,RNA-dependent RNA polymerase ,Plant Science ,biology.organism_classification ,01 natural sciences ,Genome ,humanities ,03 medical and health sciences ,030104 developmental biology ,Closterovirus ,Closteroviridae ,Agronomy and Crop Science ,Gene ,010606 plant biology & botany - Abstract
Citrus aurantifolia (acid lime) trees exhibiting yellowing, stem pitting and decline symptoms in Oman were found to be infected by Citrus tristeza virus (CTV) (genus; Closterovirus, family; Closteroviridae). The sequence of the 3′ approximately 9.8 Kb genome, encompassing the partial RNA dependent RNA polymerase to P23 genes including the 3′ UTR region was determined. Pairwise nucleotide comparisons revealed that the Oman isolate had the highest nucleotide identity with those from Mexico and Egyptian isolates. Phylogenetic analysis showed that the Oman isolate clustered with the Egyptian isolate and was identified as T36 genotype. Recombination analysis showed the presence of three potential recombination events and the findings of this study are discussed. Further, extensive studies on CTV species mainly in Oman and as a whole in the Arabian Peninsula is needed, especially after investigating the recombinant 3′ CTV genome isolate.
- Published
- 2021
32. Complete genome sequence of platycodon closterovirus 1, a novel putative member of the genus Closterovirus
- Author
-
Hye Sun Cho, Suk-Yoon Kwon, Jae Sun Moon, Hyun-Soon Kim, Jeong Mee Park, Hyo-Jun Lee, Davaajargal Igori, and Seungmo Lim
- Subjects
Whole genome sequencing ,0303 health sciences ,030306 microbiology ,Nucleic acid sequence ,General Medicine ,Platycodon grandiflorus ,Biology ,biology.organism_classification ,Virology ,Genome ,03 medical and health sciences ,Closterovirus ,ORFS ,Peptide sequence ,030304 developmental biology ,Genomic organization - Abstract
A new member of the genus Closterovirus was detected in Platycodon grandiflorus using high-throughput RNA sequencing analysis. The complete genome sequence of this new virus isolate, tentatively named “platycodon closterovirus 1” (PlaCV1), comprises 16,771 nucleotides with nine predicted open reading frames (ORFs) having the typical closterovirus genome organization. PlaCV1 shares 37%–50% nucleotide sequence identity with other known closterovirus genome sequences. The putative RNA-dependent RNA polymerase (RdRp), heat shock protein 70-like protein (HSP70h), viral heat shock protein 90-like protein (HSP90h), minor coat protein (CPm), and coat protein (CP) show 47–68%, 39–66%, 24–52%, 21–57%, and 16–35% amino acid sequence identity, respectively, to homologous proteins in previously identified closteroviruses, suggesting that it represents a distinct, new species in the genus. Phylogenetic analysis of HSP70h sequences places PlaCV1 alongside other members of the genus Closterovirus in the family Closteroviridae. To our knowledge, this study is the first report of the complete genome sequence of PlaCV1 infecting P. grandiflorus in the Republic of Korea.
- Published
- 2021
33. A Long Non-Coding RNA of Citrus tristeza virus: Role in the Virus Interplay with the Host Immunity
- Author
-
Sung-Hwan Kang, Yong-Duo Sun, Osama O. Atallah, Jose Carlos Huguet-Tapia, Jerald D. Noble, and Svetlana Y. Folimonova
- Subjects
RNA virus ,closterovirus ,Citrus tristeza virus ,long non-coding RNA ,plant immunity ,salicylic acid signaling ,alternative oxidase ,pathogenesis-related genes ,Microbiology ,QR1-502 - Abstract
During infection, Citrus tristeza virus (CTV) produces a non-coding subgenomic RNA referred to as low-molecular-weight tristeza 1 (LMT1), which for a long time has been considered as a by-product of the complex CTV replication machinery. In this study, we investigated the role of LMT1 in the virus infection cycle using a CTV variant that does not produce LMT1 (CTV-LMT1d). We showed that lack of LMT1 did not halt virus ability to replicate or form proper virions. However, the mutant virus demonstrated significantly reduced invasiveness and systemic spread in Nicotiana benthamiana as well as an inability to establish infection in citrus. Introduction of CTV-LMT1d into the herbaceous host resulted in elevation of the levels of salicylic acid (SA) and SA-responsive pathogenesis-related genes beyond those upon inoculation with wild-type (WT) virus (CTV-WT). Further analysis showed that the LMT1 RNA produced by CTV-WT or via ectopic expression in the N. benthamiana leaves suppressed SA accumulation and up-regulated an alternative oxidase gene, which appeared to mitigate the accumulation of reactive oxygen species. To the best of our knowledge, this is the first report of a plant viral long non-coding RNA being involved in counter-acting host response by subverting the SA-mediated plant defense.
- Published
- 2019
- Full Text
- View/download PDF
34. Grapefruit Field Trial Evaluation of Citrus Tristeza Virus T68-Strain Sources
- Author
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Chanel Steyn, Johan T. Burger, Rochelle de Bruyn, Hans J. Maree, Glynnis Cook, Stephanus P. van Vuuren, and Johannes H. J. Breytenbach
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Citrus ,Closterovirus ,biology ,Strain (biology) ,Citrus tristeza virus ,Effective management ,Plant Science ,biology.organism_classification ,01 natural sciences ,Genome ,Virus ,South Africa ,03 medical and health sciences ,030104 developmental biology ,Field trial ,Subject areas ,Agronomy and Crop Science ,Citrus paradisi ,Plant Diseases ,010606 plant biology & botany - Abstract
Determination of virus genomes and differentiation of strains and strain variants facilitate the linkage of biological expression to specific genetic units. For effective management of stem pitting disease of citrus tristeza virus (CTV) by cross-protection, an understanding of these links is necessary. The deliberate field application of a biological agent such as a virus first requires a thorough assessment of the long-term impact before it can be applied commercially. Three CTV sources were genetically characterized as different variants of the T68 strain, and their long-term effects on stem pitting and production were investigated. The different CTV sources were inoculated to ‘Star Ruby’ grapefruit trees and evaluated for a number of biological parameters in a field trial in the Limpopo Province of South Africa over a 10-year period. Significant differences were observed in stem pitting severity, impact on tree growth, yield, and the percentage of small fruit produced. These T68 variants were also associated with different stem pitting phenotypes. The variants differed in only 44 nucleotide positions across their genomes, and these minor genetic differences can therefore be used to identify possible genome regions affecting stem pitting.
- Published
- 2021
35. Two novel closteroviruses, fig virus A and fig virus B, identified by the analysis of the high-throughput RNA-sequencing data of fig (Ficus carica) latex
- Author
-
Yoonsoo Hahn, Chul Jun Goh, and Dongbin Park
- Subjects
Closterovirus ,Latex ,biology ,Phylogenetic tree ,High-Throughput Nucleotide Sequencing ,Ficus ,Subclade ,Genome, Viral ,General Medicine ,biology.organism_classification ,Genome ,Virology ,Virus ,Infectious Diseases ,Phylogenetics ,RNA, Viral ,Phylogeny ,Genomic organization - Abstract
Closteroviruses (the genus Closterovirus, the family Closteroviridae) are RNA viruses that infect and cause viral diseases in many economically important plants. Genome sequences of two novel closteroviruses named fig virus A (FiVA) and fig virus B (FiVB) were identified in high-throughput sequencing data obtained from a fig latex sample. FiVA and FiVB genomes, whose lengths are 19,333 bp and 18,741 bp, respectively, were predicted to have 14 shared open reading frames, nine of which had homologs in other closteroviruses. Phylogenetic analysis confirmed that FiVA and FiVB are novel closteroviruses forming a strong subclade with fig mild mottle-associated virus within the genus Closterovirus. FiVA and FiVB genome sequences identified in this study are useful resources for investigating the evolution of closterovirus genome organization. Keywords: fig virus A; fig virus B; Closterovirus; common fig; Ficus carica.
- Published
- 2021
36. Citrus miraculin‐like protein hijacks a viral movement‐related p33 protein and induces cellular oxidative stress in defence against Citrus tristeza virus
- Author
-
Yong-Duo Sun, Lei Zhang, and Svetlana Y. Folimonova
- Subjects
0106 biological sciences ,0301 basic medicine ,Citrus ,Closterovirus ,Citrus macrophylla ,p33 protein ,Plant Science ,01 natural sciences ,Virus ,03 medical and health sciences ,symbols.namesake ,Viral Proteins ,Citrus tristeza virus ,Endomembrane system ,Research Articles ,Plant Diseases ,Infectivity ,cellular oxidative stress ,biology ,Effector ,Endoplasmic reticulum ,food and beverages ,Golgi apparatus ,biology.organism_classification ,miraculin‐like protein ,Cell biology ,Oxidative Stress ,030104 developmental biology ,virus movement ,symbols ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology ,Research Article - Abstract
Summary To defend against pathogens, plants have developed a complex immune system, which recognizes the pathogen effectors and mounts defence responses. In this study, the p33 protein of Citrus tristeza virus (CTV), a viral membrane‐associated effector, was used as a molecular bait to explore virus interactions with host immunity. We discovered that Citrus macrophylla miraculin‐like protein 2 (CmMLP2), a member of the soybean Kunitz‐type trypsin inhibitor family, targets the viral p33 protein. The expression of CmMLP2 was up‐regulated by p33 in the citrus phloem‐associated cells. Knock‐down of the MLP2 expression in citrus plants resulted in a higher virus accumulation, while the overexpression of CmMLP2 reduced the infectivity of CTV in the plant hosts. Further investigation revealed that, on the one hand, binding of CmMLP2 interrupts the cellular distribution of p33 whose proper function is necessary for the effective virus movement throughout the host. On the other hand, the ability of CmMLP2 to reorganize the endomembrane system, amalgamating the endoplasmic reticulum and the Golgi apparatus, induces cellular stress and accumulation of the reactive oxygen species, which inhibits the replication of CTV. Altogether, our data suggest that CmMLP2 employs a two‐way strategy in defence against CTV infection.
- Published
- 2020
37. Closterovirus : Closteroviridae
- Author
-
Agranovsky, Alexey A., Lesemann, Dietrich-E., Tidona, Christian A., editor, Darai, Gholamreza, editor, and Büchen-Osmond, Cornelia, editor
- Published
- 2001
- Full Text
- View/download PDF
38. Viral diseases in the most widespread Balkan varieties of grapes in Kosovo.
- Author
-
DIDA, LUMTA, SHEHU, DHURATA, MEHMETI, ARBEN, and RUCI, THANAS
- Subjects
- *
VIRUS diseases of plants , *GRAPE diseases & pests , *GRAPE varieties , *VITICULTURE , *ENZYME-linked immunosorbent assay - Abstract
This study was conducted in several farms in Rahovec, Suhareka and Prizren municipalities where viniculture is developed. The following samples of varieties were selected in above mentioned regions: Afuzali, Demirkapi, Groqanka, Melnik, Pllovdin, Prokupe, Smedereve, Vranac and Zhillavk. In Rahovec region a total of 155 samples were selected, followed by the Suhareka region with 90 samples and Prizren region with a total of 5 samples. In August (2014) the labelling of samples and observation of symptoms were conducted and in January (2015) sample collection was carried out, whereas in April (2015) all samples were tested with ELISA method. All samples (300) were tested for seven viruses: Nepoviruses: (GFLV, ArMV), Closterovirus: (GLRaV-2), Ampeloviruses: (GLRaV-1, GLRaV-3), Vitivirus: (GVB) and Vitivirus: (GVA). According to the results of the ELISA test, GLRaV-3 is the most common virus with (13.3%). The second most common virus is GLRaV-1 with (8%), followed by GVA (7.3%). Regarding GFLV (2.3%) and ArMV (1%), these viruses were detected with very low incidence. None of the tested samples gave any positive reaction to GLRaV -2 and GVB. In respect of the virus distribution based on regionalization, out of 125 samples selected in Rahovec 44% came up with a positive result and out of 95 samples in Suhareka 38 were infected, whereas in Prizren only 1% samples out of 40 samples were infected. [ABSTRACT FROM AUTHOR]
- Published
- 2017
39. Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics.
- Author
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Afonso, Andreia M., Guerra, Rui, Cavaco, Ana M., Pinto, Patrícia, Andrade, André, Duarte, Amílcar, Power, Deborah M., and Marques, Natália T.
- Subjects
- *
CITRUS tristeza virus , *PLANT parasites , *FOLIAR diagnosis , *CITRUS diseases & pests , *SPECTRAL reflectance - Abstract
Citrus tristeza virus (CTV) affects citrus crops with differing severity, depending on the viral strain, the citrus cultivar and the scion/rootstock combinations. In this study we address the problem of identifying asymptomatic infected plants using reflectance spectra of the leaves in the visible/near infrared region. Sixteen young citrus plants (8 Citrus × clementina hort. ex Tanaka ‘Fina’ and 8 Citrus sinensis (L.) Osbeck ‘Valencia Late’) were split into control and T318 A isolate infected groups. Measurements of reflectance in the 400–1100 nm range, in two leaves per plant, were performed monthly over 6 months and the presence of the virus was confirmed by IC/RT-PCR and real-time PCR. The spectra acquired in a single day of measurements was inconsistent for inoculated and control plants. However, by monitoring the same leaves over 6 months it was possible to identify infected plants on the basis of the spectra time evolution. In order to achieve this a simple unfolding implementation of 3-way PCA was applied such that group separation in the scores plot was spontaneous and not forced by any a priori assumption. The model was tested through leave-one-out cross validation with a good rate of correct classification for the left out sample. A real situation was simulated by applying the NPCA algorithm to healthy plants only and checking if the infected ones would be projected on the model scores plot as outliers. Again, a good rate of classification was obtained. Finally, we discuss the spectral features that may be associated with the clustering obtained through NPCA and their physiological significance. Reflectance measurements between infected and healthy samples of two citrus cultivars and their correlation with real-time PCR results for the presence of CTV suggest reflectance spectra of the leaves in the visible/near infrared region is a promising tool for plant stress monitoring linked to the presence of CTV infection prior to symptom expression. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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40. Genetic variants of Grapevine leafroll-associated virus 2 infecting Portuguese grapevine cultivars
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Filomena FONSECA, Filipa ESTEVES, Margarida TEIXEIRA SANTOS, João BRAZÃO, and José Eduardo EIRAS-DIAS
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Closterovirus ,genetic variants ,Grapevine leafroll disease ,Botany ,QK1-989 - Abstract
Genetic variability of 19 isolates of Grapevine leafroll-associated virus 2 (GLRaV-2) from Portuguese grapevine cultivars was characterized by sequencing the entire capsid protein (CP) gene of the virus. Global phylogenetic analysis of the CP gene, which included nucleotide sequences obtained in this study and complete homologous sequences from GenBank, showed segregation of GLRaV-2 variants from Portuguese isolates into three major phylogroups (PN, 93/955 and H4). The novelty of these phylogenetic results is the evidence of well-supported subdivision within H4 as well as within PN, with subgroup PN3 composed exclusively of variants from a Portuguese isolate. These findings and the genetic analysis of global phylogroups indicate demographic expansion, mainly within PN and 93/955. Because the existence of a mixture of variants from different phylogroups was detected in some of the isolates, a typification assay based on reverse transcription reaction followed by polymerase chain reaction and restriction fragment length polymorphism analysis, was developed to complement molecular detection assay of the virus. This protocol discriminates variants from the phylogroups identified in this study, and is appropriate for routine testing for GLRaV-2.
- Published
- 2016
- Full Text
- View/download PDF
41. Development of a reverse transcription recombinase polymerase based isothermal amplification coupled with lateral flow immunochromatographic assay (CTV-RT-RPA-LFICA) for rapid detection of Citrus tristeza virus
- Author
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Siddarame Gowda, Dilip Kumar Ghosh, and Sunil B. Kokane
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0106 biological sciences ,0301 basic medicine ,Citrus ,Closterovirus ,Time Factors ,Loop-mediated isothermal amplification ,lcsh:Medicine ,Biology ,Microbiology ,01 natural sciences ,Article ,Virus ,03 medical and health sciences ,Limit of Detection ,Virology ,Complementary DNA ,lcsh:Science ,Polymerase ,Plant Diseases ,Immunoassay ,Multidisciplinary ,Biological techniques ,lcsh:R ,RNA ,Citrus tristeza virus ,food and beverages ,Reverse Transcription ,Amplicon ,biology.organism_classification ,Reverse transcriptase ,030104 developmental biology ,biology.protein ,RNA, Viral ,lcsh:Q ,Nucleic Acid Amplification Techniques ,010606 plant biology & botany - Abstract
Tristeza is a highly destructive disease of citrus caused by the phloem-limited, flexuous filamentous Citrus tristeza virus (CTV) in the genus Closterovirus and the family Closteroviridae. It has been a major constraint for higher productivity and has destroyed millions of citrus trees globally. CTV is graft transmissible and spread through use of virus infected nursery plants. Therefore, virus detection by using specific and reliable diagnostic tools is very important to mitigate disease outbreaks. Currently, the standard molecular techniques for CTV detection include RT-PCR and RT-qPCR. These diagnostic methods are highly sensitive but time consuming, labor intensive and require sophisticated expensive instruments, thus not suitable for point-of-care use. In the present study, we report the development of a rapid, sensitive, robust, reliable, and highly specific reverse transcription-RPA technique coupled with a lateral flow immunochromatographic assay (CTV-RT-RPA-LFICA). RT-RPA technique was standardized to amplify the coat protein gene of CTV (CTV-p25) and detect double labeled amplicons on a sandwich immunoassay by designing specific labeled primer pair and probe combinations. The optimally performing primer set (CTRPA-F1/CTRPA-R9-Btn) and the corresponding TwistAmp nfo probe (CTRPA-Probe) was optimized for temperature and reaction time using purified cDNA and viral RNA as template. The sensitivity of the developed assay was compared with other detection techniques using in vitro-transcribed RNA. The efficacy and specificity of the assay was evaluated using CTV positive controls, healthy samples, field grown citrus plants of unknown status, and other virus and bacterial pathogens that infect citrus plants. The RT-RPA-LFICA was able to detect ≤ 141 fg of RNA when cDNA used as a template. The assay detected ≤ 0.23 ng/µl of CTV RNA when directly used as template without cross-reactivity with other citrus pathogens. Best results were achieved at the isothermal temperature of 40 °C within 15–20 min. The study demonstrated that RT-RPA-LFICA has potential to become an improved detection technique for end users in bud-wood certification and quarantine programs and a promising platform for rapid point-of-care diagnostics for citrus farmers and small nurseries in low resource settings.
- Published
- 2020
42. Citrus Tristeza Virus Isolates of the Same Genotype Differ in Stem Pitting Severity in Grapefruit
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Coetzee B, Rachelle Bester, Glynnis Cook, Johan T. Burger, Chanel Steyn, Hans J. Maree, Rochelle de Bruyn, and Johannes H. J. Breytenbach
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0106 biological sciences ,0301 basic medicine ,Citrus ,Aphid ,Closterovirus ,Genotype ,biology ,Citrus tristeza virus ,Plant Science ,biology.organism_classification ,01 natural sciences ,Virology ,law.invention ,03 medical and health sciences ,030104 developmental biology ,Transmission (mechanics) ,law ,Animals ,Agronomy and Crop Science ,Phylogeny ,Citrus paradisi ,Plant Diseases ,010606 plant biology & botany - Abstract
Two isolates of the T68 genotype of citrus tristeza virus (CTV) were derived from a common source, GFMS12, by single aphid transmission. These isolates, named GFMS12-8 and GFMS12-1.3, induced stem pitting with differing severity in ‘Duncan’ grapefruit (Citrus × paradisi [Macfad.]). Full-genome sequencing of these isolates showed only minor nucleotide sequence differences totaling 45 polymorphisms. Numerous nucleotide changes, in relatively close proximity, were detected in the p33 open reading frame (ORF) and the leader protease domains of ORF1a. This is the first report of full-genome characterization of CTV isolates of a single genotype, derived from the same source, but showing differences in pathogenicity. The results demonstrate the development of intragenotype heterogeneity known to occur with single-stranded RNA viruses. Identification of genetic variability between isolates showing different pathogenicity will enable interrogation of specific genome regions for potential stem pitting determinants.
- Published
- 2020
43. Barley yellow dwarf virus Can Be Inoculated During Brief Intracellular Punctures in Phloem Cells Before the Sieve Element Continuous Salivation Phase
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María Arias-Martín, Jaime Jiménez, Aranzazu Moreno, Alberto Fereres, and Elisa Garzo
- Subjects
0106 biological sciences ,0301 basic medicine ,Aphid ,biology ,fungi ,Luteovirus ,food and beverages ,Plant Science ,biology.organism_classification ,01 natural sciences ,Virology ,010602 entomology ,03 medical and health sciences ,030104 developmental biology ,Barley yellow dwarf ,Rhopalosiphum padi ,Electrical penetration graph ,Closterovirus ,Hordeum vulgare ,Myzus persicae ,Agronomy and Crop Science - Abstract
The distinguished intracellular stylet puncture called phloem-pd (potential drop [pd]) produced by Myzus persicae has been associated with the transmission of the semipersistently transmitted, phloem-limited Beet yellows virus (BYV, Closterovirus). However, the production of intracellular punctures in phloem cells (phloem-pd) by other aphid species and their role in the transmission of persistently transmitted, phloem-limited viruses are still unknown. Previous studies revealed that inoculation of the persistently transmitted, phloem-limited Barley yellow dwarf virus (BYDV, Luteovirus) is associated mainly with the sieve element continuous salivation phase (E1 waveform). However, the role of brief intracellular punctures that occur before the E1 phase in the inoculation of BYDV by aphids is unknown. We aimed to investigate whether the bird cherry-oat aphid Rhopalosiphum padi (Hemiptera: Aphididae) produced a stereotypical phloem-pd and to study its role in the inoculation of BYDV. The feeding behavior of viruliferous R. padi individuals in barley (Hordeum vulgare) was monitored via the electrical penetration graph (EPG) technique. The feeding process was artificially terminated after the observation of specific EPG waveforms: standard-pds, phloem-pd, and E1. Analysis of the EPG recordings revealed the production of a phloem-pd pattern by R. padi, in addition to a short, distinct E1-like pattern (short-E1), both resulting in successful inoculation of BYDV. Also, the transmission efficiency of BYDV was directly proportional to the time spent by aphids in intracellular salivation in phloem cells. Finally, we discussed the main differences between the inoculation process of semipersistent and persistently transmitted phloem-limited viruses by aphids.
- Published
- 2020
44. Transcriptomic Analysis of the Host Response to Mild and Severe CTV Strains in Naturally Infected
- Author
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José Abrahán, Ramírez-Pool, Beatriz, Xoconostle-Cázares, Berenice, Calderón-Pérez, Enrique, Ibarra-Laclette, Emanuel, Villafán, Rosalía, Lira-Carmona, and Roberto, Ruiz-Medrano
- Subjects
Gene Expression Regulation, Viral ,Viral Proteins ,Closterovirus ,Virulence ,Gene Expression Regulation, Plant ,Gene Expression Profiling ,RNA-Seq ,Mexico ,Citrus sinensis ,Disease Resistance ,Plant Diseases ,Plant Proteins ,Plant Viruses - Published
- 2022
45. Molecular characterization of Cordyline virus 1 isolates infecting yam (Dioscorea spp)
- Author
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Mame Boucar Diouf, Olyvia Gaspard, Armelle Marais, Denis Filloux, Rose‑Marie Gomez, Chantal Faure, Philippe Roumagnac, Thierry Candresse, Sébastien Theil, Sandy Contreras, Pierre‑Yves Teycheney, and Marie Umber
- Subjects
Génétique moléculaire ,Clostérovirus ,Cordyline ,Dioscorea ,Genetic Variation ,General Medicine ,PCR ,Virology ,Transcription inverse ,Phylogeny ,H20 - Maladies des plantes ,Closteroviridae - Abstract
Cordyline virus 1 (CoV1) is a velarivirus that has so far only been reported in ornamental Ti plants (Cordyline fruticosa). Using high-throughput sequencing, we identified CoV1 infection in yam accessions from Vanuatu. Using a specific RT-PCR assay, we found that CoV1 is also present and highly prevalent in Dioscorea alata, D. cayenensis, and D. trifida in Guadeloupe. Phylogenetic analysis showed that CoV1 isolates infecting yam in Guadeloupe display a low level of molecular diversity. These data provide insights into the transmission of CoV1 in yam in Guadeloupe.
- Published
- 2022
46. Complete genome sequence of cnidium closterovirus 1, a novel member of the genus Closterovirus infecting Cnidium officinale
- Author
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Workitu Firomsa, Gudeta, Mesele Tilahun, Belete, Davaajargal, Igori, Se Eun, Kim, and Jae Sun, Moon
- Subjects
Open Reading Frames ,Closterovirus ,RNA, Viral ,Genome, Viral ,Cnidium ,Phylogeny - Abstract
The genome of a novel virus identified in Cnidium officinale is composed of a monopartite ssRNA of 16,755 nucleotides that shares 68.73% (query coverage, 20%) sequence identity with carrot yellow leaf virus (CYLV, accession no. FJ869862.1). It contains 11 putative open reading frames and has an organization typical of closteroviruses. It shares 30-50% nucleotide sequence identity with other closteroviruses. The heat shock protein 70-like protein (HSP70), putative RNA-dependent RNA polymerase (RdRp), and coat protein (CP) show 39-66%, 16-60%, and 24-41% amino acid sequence identity, respectively, to the homologous proteins of previously identified closteroviruses. Molecular and HSP70-based phylogenetic analysis of the genome and encoded protein sequences suggested that this virus is a novel member of the genus Closterovirus in the family Closteroviridae, which we have tentatively named "cnidium closterovirus 1" (CnClV1).
- Published
- 2021
47. From the smallest to the largest subcellular plant pathogen: Citrus tristeza virus and its unique p23 protein
- Author
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Pedro Moreno, Carmelo López, Susana Ruiz-Ruiz, Leandro Peña, and José Guerri
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Cancer Research ,p23-transgenic citrus ,Citrus ,Closterovirus ,CTV pathogenicity ,CTV resistance ,History, 20th Century ,Virus-host interactions ,Plants, Genetically Modified ,F60 Plant physiology and biochemistry ,History, 21st Century ,p23 subcellular localization ,Infectious Diseases ,p23 protein ,Virology ,H20 Plant diseases ,Plant Diseases - Abstract
Knowledge on diseases caused by Citrus tristeza virus (CTV) has greatly increased in last decades after their etiology was demonstrated in the past seventies. Professor Ricardo Flores substantially contributed to these advances in topics like: I) improvement of virus purification to obtain biologically active virions, II) sequencing mild CTV isolates for genetic comparisons with sequences of moderate or severe isolates and genetic engineering, III) analysis of genetic variation of both CTV genomic RNA ends and features of the highly variable 5′ end that allow accommodating this variation within a conserved secondary structure, IV) studies on the structure, subcellular localization and biological functions of the CTV-unique p23 protein, and v) potential use of p23 and other 3′ -proximal regions of the CTV genome to develop transgenic citrus resistant to the virus. Here we review his main achievements on these topics and how they contributed to deeper understanding of CTV biology and to new potential measures for disease control.
- Published
- 2021
48. First Report of Soybean Dwarf Virus Infecting White Clover (Trifolium repens) in Finland
- Author
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Johanna Santala, Mikko T. Lehtonen, Annika Luoto, and Jari P. T. Valkonen
- Subjects
0106 biological sciences ,0303 health sciences ,Aphid ,biology ,food and beverages ,RNA virus ,Plant Science ,biology.organism_classification ,01 natural sciences ,Virus ,3. Good health ,Acyrthosiphon pisum ,03 medical and health sciences ,Horticulture ,GenBank ,Trifolium repens ,Soybean dwarf virus ,Closterovirus ,Agronomy and Crop Science ,030304 developmental biology ,010606 plant biology & botany - Abstract
Soybean dwarf virus (SbDV, genus Luteovirus) is a single-stranded positive-sense RNA virus able to infect several legume species. SbDV was first reported in Japan where it was associated with significant yield losses in soybean (Tamada, 1969). Since then the virus has been detected worldwide. In Europe, the virus has only been reported from Germany (Abraham et al. 2007; Gaafar et al. 2020). In July 2018, several white clover plants (Trifolium repens L.) with leaf discoloration were observed in different locations in Oulu region in northern Finland. Individual plants were collected and analysed for the presence of viruses using small-RNA (sRNA) sequencing (Kreuze et. al. 2009) and reverse transcription-PCR (RT-PCR). Total RNA was extracted using EZNA micro RNA kit (Omega Bio-Tek, GA, USA). For sRNA analysis, sequencing libraries were constructed using the TruSeq small RNA library prep kit (Illumina, CA, USA) and sequenced on Illumina MiSeq platform. On average, 1.3 million single-end reads were obtained per sample, of which 27% were 18-25 nt long and used for the subsequent analysis. Contig assembly and virus identification with VirusDetect software (Zheng et al. 2017) detected SbDV in five out of six white clover samples analysed. Depending on the sample, 26-39 contigs (with lengths up to 301-469 nt) aligned to complete genome of a SbDV isolate previously described from white clover in USA (accession no. JN674402). The cumulative alignment coverage ranged from 35.5 % to 65.3 % with nucleotide identities between 94.4 % and 97.3 %. Additionally, two samples seemed to contain an unidentified closterovirus and one contained White clover cryptic virus 2. No additional viruses were detected from two of the samples.To confirm the presence of SbDV, the samples were tested by RT-PCR using primers MDF, MYF and MUR in multiplex (Schneider et al. 2011) together with SuperScript III One-Step RT-PCR System with the Platinum Taq DNA polymerase kit (Thermo Fisher Scientific, USA), essentially as instructed by the manufacturer. RT-PCR product of approximately 400 bp was produced from each of the five samples previously tested SbDV positive by sRNA analysis. No products were produced from the sample that was SbDV negative in sRNA analysis. Direct sequencing of two of the PCR products produced 347 and 361 bp sequences (GenBank: MZ355392 and MW929169) that were 95.7 % and 95.2 % identical, respectively, to a SbDV isolate (accession no. AB038148) that causes yellowing on soybean and is transmitted by Acyrthosiphon pisum (Terauchi et al. 2003). To our knowledge this is the first report of SbDV in Finland. SbDV is transmitted only by aphids (neither mechanical nor seed transmission occurs). In siRNA analysis all the isolates from Finland formed contigs that aligned almost perfectly (100 % coverage with ≥ 99 % nucleotide identity) to the coat protein (accession no. EF466131) of an SbDV isolate transmittable from white clover to faba bean by A. pisum (Abraham et al. 2007), an aphid common in Finland. Although significant yield losses by SbDV have only been reported on soybean (Tamada, 1969), the virus also causes symptoms in other legume crops, such as growth reduction on pea (Tian et al. 2017) and faba bean (Abraham et al. 2007), both of which are cultivated in Finland. References: Abraham et al. 2007. Plant Dis. 91: 1059. Gaafar et al. 2020. Front microbiol. 11: 583242. Kreuze et al. 2009. Virology 388:1. Schneider et al. 2011. Virology 412: 46. Tamada. 1969. Ann Phytopathol Soc Jpn. 35: 282. Terauchi et al. 2003. Phytopathology 93: 1560. Tian et al. 2017. Viruses 9: 155. Zheng et al. 2017. Virology 500: 130.
- Published
- 2021
49. Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species
- Author
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Igor Koloniuk, Thanuja Thekke-Veetil, Jean-Sébastien Reynard, Irena Mavrič Pleško, Jaroslava Přibylová, Justine Brodard, Isabelle Kellenberger, Tatiana Sarkisova, Josef Špak, Janja Lamovšek, Sebastien Massart, Thien Ho, Joseph D. Postman, and Ioannis E. Tzanetakis
- Subjects
Ribes ,currant ,closterovirus ,recombinants/recombination ,Microbiology ,QR1-502 - Abstract
Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination.
- Published
- 2018
- Full Text
- View/download PDF
50. Diversity of Uruguayan citrus tristeza virus populations segregated after single aphid transmission
- Author
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Hernández-Rodríguez, Lester, Benítez-Galeano, María José, Bertalmío, Ana, Rubio, Leticia, Rivas, Fernando, Arruabarrena, Ana, Rolón, Rodolfo, Colina, Rodney, and Maeso, Diego
- Published
- 2019
- Full Text
- View/download PDF
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