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Adegbola RO, Keith CV, Gutierrez O, Goenaga R, Brown JK. Complete genome characterization of cacao leafroll virus, a newly described cacao-infecting polerovirus. Arch Virol 2024; 169:83. [PMID: 38521887 DOI: 10.1007/s00705-024-06013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/04/2024] [Indexed: 03/25/2024]
Abstract
The complete genome sequence of cacao leafroll virus (CaLRV; family Solemoviridae, genus Polerovirus) was determined by high-throughput sequencing of total RNA isolated from symptomatic cacao Theobroma cacao L. plants (n = 4). The CaLRV genome sequences ranged from 5,976 to 5,997 nucleotides (nt) in length and contained seven open reading frames (ORFs). Nucleotide and amino acid (aa) sequence comparisons showed that, among selected well-characterized poleroviruses, the CaLRV genome shared the highest nt sequence identity of 62% with that of potato leafroll virus (PLRV, NC_076505). A comparison of the predicted aa sequence of the CaLRV coat protein indicated that cotton leafroll dwarf virus (CLRDV, NC_014545) and melon aphid-borne yellows virus (MABYV, NC_010809) were the closest relatives, sharing 57% aa sequence identity. Bayesian phylogenetic analysis based on complete genome sequences showed that CaLRV grouped with well-characterized poleroviruses that cause diseases of cereal and vegetable crops. During the course of publishing this work, the nearly complete genome sequence of a member of the same polerovirus species, referred to as "cacao polerovirus" (OR605721), with which CaLRV shares 99% nt sequence identity, was reported.
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Affiliation(s)
- Raphael O Adegbola
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Cory V Keith
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Osman Gutierrez
- USDA-ARS Subtropical Horticultural Research Station, Miami, FL, 33158, USA
| | - Ricardo Goenaga
- USDA-ARS Tropical Agriculture Research Station, Mayaguez, PR, 00680, USA
| | - Judith K Brown
- School of Plant Sciences, The University of Arizona, Tucson, AZ, 85721, USA.
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2
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Miller WA, Lozier Z. Yellow Dwarf Viruses of Cereals: Taxonomy and Molecular Mechanisms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:121-141. [PMID: 35436423 DOI: 10.1146/annurev-phyto-121421-125135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Yellow dwarf viruses are the most economically important and widespread viruses of cereal crops. Although they share common biological properties such as phloem limitation and obligate aphid transmission, the replication machinery and associated cis-acting signals of these viruses fall into two unrelated taxa represented by Barley yellow dwarf virus and Cereal yellow dwarf virus. Here, we explain the reclassification of these viruses based on their very different genomes. We also provide an overview of viral protein functions and their interactions with the host and vector, replication mechanisms of viral and satellite RNAs, and the complex gene expression strategies. Throughout, we point out key unanswered questions in virus evolution, structural biology, and genome function and replication that, when answered, may ultimately provide new tools for virus management.
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Affiliation(s)
- W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA;
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
| | - Zachary Lozier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA;
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
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3
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Advances in RNA-Silencing-Related Resistance against Viruses in Potato. Genes (Basel) 2022; 13:genes13050731. [PMID: 35627117 PMCID: PMC9141481 DOI: 10.3390/genes13050731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
Potato is a major food crop that has the potential to feed the increasing global population. Potato is the fourth most important crop and a staple food for many people worldwide. The traditional breeding of potato poses many challenges because of its autotetraploid nature and its tendency toward inbreeding depression. Moreover, potato crops suffer considerable production losses because of infections caused by plant viruses. In this context, RNA silencing technology has been successfully applied in model and crop species. In this review, we describe the RNA interference (RNAi) mechanisms, including small-interfering RNA, microRNA, and artificial microRNA, which may be used to engineer resistance against potato viruses. We also explore the latest advances in the development of antiviral strategies to enhance resistance against potato virus X, potato virus Y, potato virus A, potato leafroll virus, and potato spindle tuber viroid. Furthermore, the challenges in RNAi that need to be overcome are described in this review. Altogether, this report would be insightful for the researchers attempting to understand the RNAi-mediated resistance against viruses in potato.
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Patton MF, Bak A, Sayre JM, Heck ML, Casteel CL. A polerovirus, Potato leafroll virus, alters plant-vector interactions using three viral proteins. PLANT, CELL & ENVIRONMENT 2020; 43:387-399. [PMID: 31758809 DOI: 10.1111/pce.13684] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 05/20/2023]
Abstract
Potato leafroll virus (PLRV), genus Polerovirus, family Luteoviridae, is a major pathogen of potato worldwide. PLRV is transmitted among host plants by aphids in a circulative-nonpropagative manner. Previous studies have demonstrated that PLRV infection increases aphid fecundity on, and attraction to, infected plants as compared to controls. However, the molecular mechanisms mediating this relationship are still poorly understood. In this study, we measured the impact of PLRV infection on plant-aphid interactions and plant chemistry in two hosts: Solanum tuberosum and Nicotiana benthamiana. Our study demonstrates that PLRV infection attenuates the induction of aphid-induced jasmonic acid and ethylene in S. tuberosum and N. benthamiana. Using transient expression experiments, insect bioassays and chemical analysis, we show that expression of three PLRV proteins (P0, P1, and P7) mediate changes in plant-aphid interactions and inhibition of aphid-induced jasmonic acid and ethylene in N. benthamiana. This study enhances our understanding of the plant-vector-pathogen interface by elucidating new mechanisms by which plant viruses transmitted in a circulative manner can manipulate plant hosts.
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Affiliation(s)
- MacKenzie F Patton
- Department of Plant Pathology, University of California, Davis, California
| | - Aurélie Bak
- Department of Plant Pathology, University of California, Davis, California
| | - Jordan M Sayre
- Department of Microbiology, University of California, Davis, California
| | - Michelle L Heck
- USDA Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York, 14853
- Boyce Thompson Institute for Plant Research, Ithaca, New York, 14853
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853
| | - Clare L Casteel
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853
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Zhang F, Yang Z, Hong N, Wang G, Wang A, Wang L. Identification and characterization of water chestnut Soymovirus-1 (WCSV-1), a novel Soymovirus in water chestnuts (Eleocharis dulcis). BMC PLANT BIOLOGY 2019; 19:159. [PMID: 31023231 PMCID: PMC6482551 DOI: 10.1186/s12870-019-1761-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. High throughput sequencing of small RNA (sRNA) combined with bioinformatics, and molecular identification based on PCR detection with virus-specific primers and DNA sequencing is a desirable approach to identify an unknown infectious agent. In this study, we employed this approach to identify viral sequences in water chestnut plants and to explore the molecular interaction of the identified viral pathogen and its natural plant host. RESULTS Based on high throughput sequencing of virus-derived small RNAs (vsRNA), we identified the sequence a new-to-science double-strand DNA virus isolated from water chestnut cv. 'Tuanfeng' samples, a widely grown cultivar in Hubei province, China, and analyzed its genomic organization. The complete genomic sequence is 7535 base-pairs in length, and shares 42-52% nucleotide sequence identity with viruses in the Caulimoviridae family. The virus contains nine predicated open reading frames (ORFs) encoding nine hypothetical proteins, with conserved domains characteristic of caulimoviruses. Phylogenetic analyses at the nucleotide and amino acid levels indicated that the virus belongs to the genus Soymovirus. The virus is tentatively named Water chestnut soymovirus-1 (WCSV-1). Phylogenetic analysis of the putative viral polymerase protein suggested that WCSV-1 is distinct to other well established species in the Soymovirus genus. This conclusion was supported by phylogenetic analyses of the amino acid sequences encoded by ORFs I, IV, VI, or VII. The sRNA bioinformatics showed that the majority of the vsRNAs are 22-nt in length with a preference for U at the 5'-terminal nucleotide. The vsRNAs are unevenly distributed over both strands of the entire WCSV-1 circular genome, and are clustered into small defined regions. In addition, we detected WCSV-1 in asymptomatic and symptomatic water chestnut samples collected from different regions of China by using PCR. RNA-seq assays further confirmed the presence of WCSV-1-derived viral RNA in infected plants. CONCLUSIONS This is the first discovery of a dsDNA virus in the genus Soymovirus infecting water chestnuts. Data presented also add new information towards a better understanding of the co-evolutionary mechanisms between the virus and its natural plant host.
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Affiliation(s)
- Fangpeng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Zuokun Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 Canada
| | - Liping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
- Lab of Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei People’s Republic of China
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Rashid MO, Zhang XY, Wang Y, Li DW, Yu JL, Han CG. The Three Essential Motifs in P0 for Suppression of RNA Silencing Activity of Potato leafroll virus Are Required for Virus Systemic Infection. Viruses 2019; 11:E170. [PMID: 30791535 PMCID: PMC6410027 DOI: 10.3390/v11020170] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/14/2019] [Accepted: 02/16/2019] [Indexed: 12/19/2022] Open
Abstract
Higher plants exploit posttranscriptional gene silencing as a defense mechanism against virus infection by the RNA degradation system. Plant RNA viruses suppress posttranscriptional gene silencing using their encoded proteins. Three important motifs (F-box-like motif, G139/W140/G141-like motif, and C-terminal conserved region) in P0 of Potato leafroll virus (PLRV) were reported to be essential for suppression of RNA silencing activity. In this study, Agrobacterium-mediated transient experiments were carried out to screen the available amino acid substitutions in the F-box-like motif and G139/W140/G141-like motif that abolished the RNA silencing suppression activity of P0, without disturbing the P1 amino acid sequence. Subsequently, four P0 defective mutants derived from a full-length cDNA clone of PLRV (L76F and W87R substitutions in the F-box-like motif, G139RRR substitution in the G139/W140/G141-like motif, and F220R substitution in the C-terminal conserved region) were successfully generated by reverse PCR and used to investigate the impact of these substitutions on PLRV infectivity. The RT-PCR and western blot analysis revealed that these defective mutants affected virus accumulation in inoculated leaves and systemic movement in Nicotiana benthamiana as well as in its natural hosts, potato and black nightshade. These results further demonstrate that the RNA silencing suppressor of PLRV is required for PLRV accumulation and systemic infection.
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Affiliation(s)
- Mamun-Or Rashid
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management, MOA, China Agricultural University, Beijing 100193, China.
| | - Xiao-Yan Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management, MOA, China Agricultural University, Beijing 100193, China.
| | - Ying Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management, MOA, China Agricultural University, Beijing 100193, China.
| | - Da-Wei Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management, MOA, China Agricultural University, Beijing 100193, China.
| | - Jia-Lin Yu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management, MOA, China Agricultural University, Beijing 100193, China.
| | - Cheng-Gui Han
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management, MOA, China Agricultural University, Beijing 100193, China.
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Xu Y, Da Silva WL, Qian Y, Gray SM. An aromatic amino acid and associated helix in the C-terminus of the potato leafroll virus minor capsid protein regulate systemic infection and symptom expression. PLoS Pathog 2018; 14:e1007451. [PMID: 30440046 PMCID: PMC6264904 DOI: 10.1371/journal.ppat.1007451] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 11/29/2018] [Accepted: 11/01/2018] [Indexed: 12/26/2022] Open
Abstract
The C-terminal region of the minor structural protein of potato leafroll virus (PLRV), known as the readthrough protein (RTP), is involved in efficient virus movement, tissue tropism and symptom development. Analysis of numerous C-terminal deletions identified a five-amino acid motif that is required for RTP function. A PLRV mutant expressing RTP with these five amino acids deleted (Δ5aa-RTP) was compromised in systemic infection and symptom expression. Although the Δ5aa-RTP mutant was able to move long distance, limited infection foci were observed in systemically infected leaves suggesting that these five amino acids regulate virus phloem loading in the inoculated leaves and/or unloading into the systemically infected tissues. The 5aa deletion did not alter the efficiency of RTP translation, nor impair RTP self-interaction or its interaction with P17, the virus movement protein. However, the deletion did alter the subcellular localization of RTP. When co-expressed with a PLRV infectious clone, a GFP tagged wild-type RTP was localized to discontinuous punctate spots along the cell periphery and was associated with plasmodesmata, although localization was dependent upon the developmental stage of the plant tissue. In contrast, the Δ5aa-RTP-GFP aggregated in the cytoplasm. Structural modeling indicated that the 5aa deletion would be expected to perturb an α-helix motif. Two of 30 plants infected with Δ5aa-RTP developed a wild-type virus infection phenotype ten weeks post-inoculation. Analysis of the virus population in these plants by deep sequencing identified a duplication of sequences adjacent to the deletion that were predicted to restore the α-helix motif. The subcellular distribution of the RTP is regulated by the 5-aa motif which is under strong selection pressure and in turn contributes to the efficient long distance movement of the virus and the induction of systemic symptoms.
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Affiliation(s)
- Yi Xu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Washington Luis Da Silva
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Yajuan Qian
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Stewart M. Gray
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY, United States of America
- Emerging Pest and Pathogens Research Unit, USDA, ARS, Ithaca, NY, United States of America
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8
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Fusaro AF, Barton DA, Nakasugi K, Jackson C, Kalischuk ML, Kawchuk LM, Vaslin MFS, Correa RL, Waterhouse PM. The Luteovirus P4 Movement Protein Is a Suppressor of Systemic RNA Silencing. Viruses 2017; 9:v9100294. [PMID: 28994713 PMCID: PMC5691645 DOI: 10.3390/v9100294] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 11/16/2022] Open
Abstract
The plant viral family Luteoviridae is divided into three genera: Luteovirus, Polerovirus and Enamovirus. Without assistance from another virus, members of the family are confined to the cells of the host plant's vascular system. The first open reading frame (ORF) of poleroviruses and enamoviruses encodes P0 proteins which act as silencing suppressor proteins (VSRs) against the plant's viral defense-mediating RNA silencing machinery. Luteoviruses, such as barley yellow dwarf virus-PAV (BYDV-PAV), however, have no P0 to carry out the VSR role, so we investigated whether other proteins or RNAs encoded by BYDV-PAV confer protection against the plant's silencing machinery. Deep-sequencing of small RNAs from plants infected with BYDV-PAV revealed that the virus is subjected to RNA silencing in the phloem tissues and there was no evidence of protection afforded by a possible decoy effect of the highly abundant subgenomic RNA3. However, analysis of VSR activity among the BYDV-PAV ORFs revealed systemic silencing suppression by the P4 movement protein, and a similar, but weaker, activity by P6. The closely related BYDV-PAS P4, but not the polerovirus potato leafroll virus P4, also displayed systemic VSR activity. Both luteovirus and the polerovirus P4 proteins also showed transient, weak local silencing suppression. This suggests that systemic silencing suppression is the principal mechanism by which the luteoviruses BYDV-PAV and BYDV-PAS minimize the effects of the plant's anti-viral defense.
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Affiliation(s)
- Adriana F Fusaro
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- Plant Industry Division, CSIRO, P.O. Box 1600, Canberra, ACT 2601, Australia.
- Department of Virology (M.F.S.V.), Department of Genetics (R.L.C.) and Institute of Medical Biochemistry (A.F.F.), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil.
| | - Deborah A Barton
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Kenlee Nakasugi
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Craig Jackson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Melanie L Kalischuk
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA.
| | - Lawrence M Kawchuk
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- Department of Agriculture and Agri-Food Canada, Lethbridge, AB T1J4B1, Canada.
| | - Maite F S Vaslin
- Department of Virology (M.F.S.V.), Department of Genetics (R.L.C.) and Institute of Medical Biochemistry (A.F.F.), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil.
| | - Regis L Correa
- Plant Industry Division, CSIRO, P.O. Box 1600, Canberra, ACT 2601, Australia.
- Department of Virology (M.F.S.V.), Department of Genetics (R.L.C.) and Institute of Medical Biochemistry (A.F.F.), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, Brazil.
| | - Peter M Waterhouse
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
- Plant Industry Division, CSIRO, P.O. Box 1600, Canberra, ACT 2601, Australia.
- School of Earth, Environmental and Biological sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia.
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9
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Zhang P, Liu Y, Liu W, Cao M, Massart S, Wang X. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease. Front Microbiol 2017; 8:1689. [PMID: 28932215 PMCID: PMC5592212 DOI: 10.3389/fmicb.2017.01689] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/21/2017] [Indexed: 11/13/2022] Open
Abstract
To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.
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Affiliation(s)
- Peipei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-Bio TechGembloux, Belgium
| | - Yan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-Bio TechGembloux, Belgium
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
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10
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Zhou CJ, Zhang XY, Liu SY, Wang Y, Li DW, Yu JL, Han CG. Synergistic infection of BrYV and PEMV 2 increases the accumulations of both BrYV and BrYV-derived siRNAs in Nicotiana benthamiana. Sci Rep 2017; 7:45132. [PMID: 28345652 PMCID: PMC5366869 DOI: 10.1038/srep45132] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Viral synergism is caused by co-infection of two unrelated viruses, leading to more severe symptoms or increased titres of one or both viruses. Synergistic infection of phloem-restricted poleroviruses and umbraviruses has destructive effects on crop plants. The mechanism underlying this synergy remains elusive. In our study, synergism was observed in co-infections of a polerovirus Brassica yellows virus (BrYV) and an umbravirus Pea enation mosaic virus 2 (PEMV 2) on Nicotiana benthamiana, which led to (1) increased titres of BrYV, (2) appearance of severe symptoms, (3) gain of mechanical transmission capacity of BrYV, (4) broader distribution of BrYV to non-vascular tissues. Besides, profiles of virus-derived small interfering RNAs (vsiRNAs) from BrYV and PEMV 2 in singly and doubly infected plants were obtained by small RNA deep sequencing. Our results showed that accumulation of BrYV vsiRNAs increased tremendously and ratio of positive to negative strand BrYV vsiRNAs differed between singly infected and co-infected plants. Positions to which the BrYV vsiRNAs mapped to the viral genome varied considerably during synergistic infection. Moreover, target genes of vsiRNAs were predicted and annotated. Our results revealed the synergistic characteristics during co-infection of BrYV and PEMV 2, and implied possible effects of synergism have on vsiRNAs.
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Affiliation(s)
- Cui-Ji Zhou
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
| | - Xiao-Yan Zhang
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
| | - Song-Yu Liu
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
| | - Ying Wang
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
| | - Da-Wei Li
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
| | - Jia-Lin Yu
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
| | - Cheng-Gui Han
- State Key Laboratory for Agro-Biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, P. R. China
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11
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Roossinck MJ, Martin DP, Roumagnac P. Plant Virus Metagenomics: Advances in Virus Discovery. PHYTOPATHOLOGY 2015; 105:716-27. [PMID: 26056847 DOI: 10.1094/phyto-12-14-0356-rvw] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems-aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.
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Affiliation(s)
- Marilyn J Roossinck
- First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Darren P Martin
- First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Philippe Roumagnac
- First author: Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; second author: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925 South Africa; and third author: CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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Kutnjak D, Silvestre R, Cuellar W, Perez W, Müller G, Ravnikar M, Kreuze J. Complete genome sequences of new divergent potato virus X isolates and discrimination between strains in a mixed infection using small RNAs sequencing approach. Virus Res 2014; 191:45-50. [PMID: 25051147 DOI: 10.1016/j.virusres.2014.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/09/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Potato virus X (PVX; genus Potexvirus, family Alphaflexiviridae, order Tymovirales) is one of the most widespread and intensively studied viruses of potato. However, little is known about its diversity in its likely center of radiation, the Andean region of South America. To fill this gap, the strategy of Illumina deep sequencing of small RNAs was used to obtain complete or near complete genome sequence of PVX from 5 symptomatically infected greenhouse and 3 field samples (Solanum tuberosum) from Peru. PVX sequences determined in this study were assigned into three different phylogenetic groups of isolates. Notably, a complete genome sequence of a representative of a new PVX phylogenetic lineage was obtained, which shows a high level of sequence dissimilarity to other completely sequenced isolates (∼17%). The new PVX genotype was detected in greenhouse and field samples. One of the field samples was infected with the mixture of two PVX strains, which were efficiently discriminated using small RNA sequencing approach. The study confirms the utility of small RNAs deep sequencing for successful viral strain differentiation and discovery of new viral strains and indicates a high diversity of PVX in the Andean region of South America, a pattern which may be expected also for other potato pathogens.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | | | | | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Jan Kreuze
- International Potato Center (CIP), Lima, Peru.
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Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R. Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Res 2014; 186:20-31. [DOI: 10.1016/j.virusres.2013.12.007] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/08/2013] [Accepted: 12/09/2013] [Indexed: 01/02/2023]
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14
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Kalischuk ML, Fusaro AF, Waterhouse PM, Pappu HR, Kawchuk LM. Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs. Virus Res 2013; 178:306-13. [PMID: 24076299 DOI: 10.1016/j.virusres.2013.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Abstract
Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants.
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Affiliation(s)
- Melanie L Kalischuk
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-106, United States; Agriculture and Agri-Food Canada, P.O. Box 3000, Lethbridge, Alberta T1J 4B1, Canada
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