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Wang M, Su X, Zhang F, Wang T, Zheng K, Zhang Z. Complete genome sequence of polygonatum kingianum mottle virus infecting Polygonatum kingianum Coll. et Hemsl in Yunnan, China. Arch Virol 2024; 169:39. [PMID: 38300368 DOI: 10.1007/s00705-024-05965-0] [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: 09/20/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024]
Abstract
The complete genome sequence of a putative novel potyvirus, tentatively named "polygonatum kingianum mottle virus" (PKgMV; GenBank accession no. ON428226), infecting Polygonatum kingianum in China, was obtained by next-generation sequencing (NGS), reverse transcription polymerase chain reaction (RT-PCR), and rapid amplification of cDNA ends (RACE). PKgMV exhibits the typical genome organization and characteristics of members of the genus Potyvirus, with a length of 10,002 nucleotides (nt) and a large open reading frame (nt 108 to 9,746) encoding a polyprotein of 3,212 amino acids (aa) (363.68 kDa). Pairwise comparisons revealed that the PKgMV polyprotein shares 50.5-68.6% nt and 43.1-72.2% aa sequence identity with reported members of the genus Potyvirus. Moreover, phylogenetic analysis indicated that PKgMV is closely related to polygonatum kingianum virus 1 (PKgV1; accession no. MK427056). These results suggest that the PKgMV is a novel member of the genus Potyvirus of the family Potyviridae.
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Affiliation(s)
- Maosen Wang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, Yunnan, 650205, P. R. China
- School of Agriculture, Yunnan University, Kunming, Yunnan, 650091, P. R. China
| | - Xiaoxia Su
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, Yunnan, 650205, P. R. China
| | - Fan Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, Yunnan, 650205, P. R. China
- School of Agriculture, Yunnan University, Kunming, Yunnan, 650091, P. R. China
| | - Tiantian Wang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, Yunnan, 650205, P. R. China
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, Yunnan, 650205, P. R. China.
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming, Yunnan, 650205, P. R. China.
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Yang J, Lan PX, Wang Y, Li JM, Li R, Wylie S, Chen XJ, Yang GH, Cai H, Li F. Virome Analysis of Aconitum carmichaelii Reveals Infection by Eleven Viruses, including Two Potentially New Species. Int J Mol Sci 2023; 24:15558. [PMID: 37958540 PMCID: PMC10650655 DOI: 10.3390/ijms242115558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Aconitum carmichaelii is a herbaceous herb indigenous to China that has been cultivated for traditional medicine for centuries. Virus-like symptoms of A. carmichaelii plants were observed on leaves in some A. carmichaelii plantations in Zhanyi and Wuding Counties, Yunnan Province, southwest China. High-throughput sequencing (HTS) was performed on 28 symptomatic plants, and the results revealed infection with 11 viruses, including 2 novel viruses and 9 previously described viruses: Aconitum amalgavirus 1 (AcoAV-1), aconite virus A (AcVA), cucumber mosaic virus (CMV), currant latent virus (CuLV), apple stem grooving virus (ASGV), chilli veinal mottle virus (ChiVMV), tomato spotted wilt orthotospovirus (TSWV), tobacco vein distorting virus (TVDV), and potato leafroll virus (PLRV). Two novel viruses tentatively named Aconitum potyvirus 1 and Aconitum betapartitivirus 1, were supported by sequence and phylogenetic analysis results of their genomes. We proposed the names Potyvirus aconiti and Betapartitivirus aconiti. RT-PCR assays of 142 plants revealed the predominance and widespread distribution of CMV, AcVA, and AcoPV-1 in plantations. The detection of isolates of CuLV, ASGV, ChiVMV, TSWV, TVDV, and PLRV infections for the first time in A. carmichaelii expands their known host ranges.
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Affiliation(s)
- Jie Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Ping-Xiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Yun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Jin-Ming Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA
| | - Steve Wylie
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
| | - Xiao-Jiao Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Gen-Hua Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Hong Cai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
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Complete genome sequence of polygonatum mosaic-associated virus 1, a novel member of the genus Potyvirus in China. Arch Virol 2023; 168:42. [PMID: 36609607 DOI: 10.1007/s00705-022-05665-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/09/2022] [Indexed: 01/09/2023]
Abstract
The complete genome sequence of a putative novel potyvirus, tentatively named "polygonatum mosaic-associated virus 1" (PMaV1), was sequenced from naturally infected Polygonatum cyrtonema Hua in China. PMaV1 has a typical genome organization of potyviruses with a single large open reading frame (nt 119-9448) that encodes a 3109-aa polyprotein that is predicted to be cleaved into 10 mature proteins by virus-encoded proteases. Pairwise comparisons revealed that PMaV1 shares 71.50% complete genome sequence identity with Polygonatum kingianum virus 4 and 80.00% amino acid sequence identity with Polygonatum kingianum virus 3 of the genus Potyvirus. Phylogenetic analysis indicated that PMaV1 clustered with other potyviruses and that it was most closely related to Polygonatum kingianum virus 3 and Polygonatum kingianum virus 4. These results suggest that PMaV1 is a new member of the genus Potyvirus of the family Potyviridae (Nucleotide sequence data reported are available in the GenBank databases under the accession number OP380926).
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Igori D, Shin AY, Kim SE, Choi EK, Hwang US, Kwon SY, Moon JS. Complete genome sequence and genome characterization of a novel potyvirus from Lamprocapnos spectabilis. Arch Virol 2023; 168:25. [PMID: 36593436 DOI: 10.1007/s00705-022-05654-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/25/2022] [Indexed: 01/04/2023]
Abstract
The genome of a new potyvirus from a Lamprocapnos spectabilis plant in South Korea was sequenced by high-throughput sequencing and confirmed by Sanger sequencing. The new potyvirus was tentatively named "lamprocapnos virus A" (LaVA); its complete genome contains 9,745 nucleotides, excluding the 3'-terminal poly(A) tail. The LaVA genome structure is similar to that of members of the genus Potyvirus and contains an open reading frame encoding a large putative polyprotein of 3,120 amino acids (aa) with conserved motifs. The complete genome shared 48%-56% nucleotide sequence identity and the polyprotein shared 41%-52% aa sequence identity with those of other potyviruses. These values are below the standard thresholds for potyvirus species demarcation. Phylogenetic analysis based on polyprotein sequences showed that LaVA belongs to the genus Potyvirus. To our knowledge, this is the first report of the complete genome sequence and genome characterization of a potyvirus infecting Lamprocapnos spectabilis.
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Affiliation(s)
- Davaajargal Igori
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia.,Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Se-Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Eung Kyoo Choi
- Jangchun Seed Company, 72 Sideok-ro, Chilgok-gun, Yakmokmyeon, Kyeongsangbuk-do, 39821, Republic of Korea
| | - Un Sun Hwang
- Jangchun Seed Company, 72 Sideok-ro, Chilgok-gun, Yakmokmyeon, Kyeongsangbuk-do, 39821, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Lan PX, He P, Yang J, Zhou GH, Chen XJ, Wei TY, Li CR, Gu R, Li R, Li F. High-throughput sequencing reveals the presence of novel and known viruses in diseased Paris yunnanensis. Front Microbiol 2022; 13:1045750. [PMID: 36590431 PMCID: PMC9795479 DOI: 10.3389/fmicb.2022.1045750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/21/2022] [Indexed: 01/03/2023] Open
Abstract
Paris spp. are important medicinal plant and main raw material for many Chinese patent medicines, but viral diseases have became serious problems in cultivation of this group of important medicinal plants in China. In this study, eight viruses were identified in the diseased plants of Paris yunnanensis by high-throughput sequencing (HTS) and RT-PCR. These viruses include three novel viruses (two potyviruses and one nepovirus), Hippeastrum chlorotic ringspot virus (HCRV), Lychnis mottle virus (LycMoV), Paris mosaic necrosis virus (PMNV), Paris virus 1 and pepper mild mottle virus. The three new viruses were tentatively named Paris potyvirus 3 (ParPV-3), Paris potyvirus 4 (ParPV-4), Paris nepovirus 1 (ParNV-1) and their complete genome sequences were determined. Sequence analyses showed ParPV-3 and ParPV-4 shared the highest amino acid (aa) sequence identities of 54.3% to each other and 53.0-57.8% to other known potyviruses. ParNV-1 had aa sequence identities of 28.8-63.7% at protease-polymerase (Pro-Pol) with other nepoviruses. Phylogenetic analyses further support that the three viruses are new members of their corresponding genera. Analyses of the partial sequences of HCRV and LycMoV infecting P. yunnanensis revealed they diverged from existing isolates by aa sequence identities of 97.1% at glycoprotein precursor of HCRV and 93.3% at polyprotein of LycMoV. These two viruses are reported for the first time in Paris spp. A total of 123 field samples collected from P. yunnanensis in four counties of Yunnan, Southwest China were tested by RT-PCR for detecting each of the eight viruses. Results showed that nearly half of the samples were positive for at least one of the eight viruses. Two potyviruses, ParPV-3 (26.8%) and PMNV (24.4%), were predominant and widely distributed in the fields, while other viruses occurred in low rates and/or had limited distribution. This study insights into the virome infecting P. yunnanensis and provides valuable information for diagnosis and control of viral diseases in P. yunnanensis.
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Affiliation(s)
- Ping-xiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Peng He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Jie Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Guo-hua Zhou
- Yunnan Baiyao Group, Chinese Medicine Resources Co., Ltd., Kunming, China
| | - Xiao-jiao Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Tai-yun Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chen-rong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Rong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, United States,*Correspondence: Ruhui Li,
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China,Fan Li,
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Prajapati MR, Manav A, Singhal P, Sidharthan VK, Sirohi U, Kumar M, Bharti MK, Singh J, Kumar P, Kumar R, Prakash S, Baranwal VK. Complete Genomic RNA Sequence of Tuberose Mild Mosaic Virus and Tuberose Mild Mottle Virus Acquired by High-Throughput Sequencing. Pathogens 2022; 11:pathogens11080861. [PMID: 36014982 PMCID: PMC9412269 DOI: 10.3390/pathogens11080861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Tuberose (Polianthes tuberosa) is an ornamental flowering crop of the Amaryllidaceae family. Tuberose mild mosaic virus (TuMMV) and tuberose mild mottle virus (TuMMoV), members of the genus Potyvirus, are ubiquitously distributed in most tuberose growing countries worldwide with low biological incidence. Here, we report the first coding-complete genomic RNA of TuMMV and TuMMoV obtained through high-throughput sequencing (HTS) and further, the presence of both the viruses were confirmed using virus-specific primers in RT-PCR assays. Excluding the poly (A) tail, the coding-complete genomic RNA of TuMMV and TuMMoV was 9485 and 9462 nucleotides (nts) in length, respectively, and contained a single large open reading frame (ORF). Polyprotein encoded by both the viral genomes contained nine putative cleavage sites. BLASTn analysis of TuMMV and TuMMoV genomes showed 72.40–76.80% and 67.95–77% nucleotide sequence similarities, respectively, with the existing potyviral sequences. Phylogenetic analysis based on genome sequences showed that TuMMV and TuMMoV clustered in a distinct clade to other potyviruses. Further studies are required to understand the mechanism of symptom development, distribution, genetic variability, and their possible threat to tuberose production in India.
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Affiliation(s)
- Malyaj R Prajapati
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Aakansha Manav
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Pankhuri Singhal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Venkidusamy K Sidharthan
- Division of Genetics and Tree Improvement, Institute of Forest Biodiversity (ICFRE), Hyderabad 500100, Telangana, India
| | - Ujjwal Sirohi
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Mukesh Kumar
- College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Mahesh Kumar Bharti
- College of Veterinary and Animal Science, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Jitender Singh
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Pankaj Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Ravindra Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Satya Prakash
- College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Virendra Kumar Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Characterization of a new potyvirus infecting Thevetia ahouai in Ecuador. Arch Virol 2022; 167:1461-1466. [PMID: 35469094 DOI: 10.1007/s00705-022-05450-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 11/02/2022]
Abstract
A new potyvirus was found in Thevetia ahouai L. (Fam. Apocynaceae) plants exhibiting white spots on leaves and fruit discoloration in Ecuador. The complete genome sequences of two isolates of this virus, tentatively named "thevetia white spot virus" (ThWSV), were determined and found to be 9,912 (isolate 1) and 9,904 (isolate 2) nucleotides (nt) in length, each encoding a polyprotein of 363 kDa. Sequence comparisons between the two isolates showed 80 and 87% identity at the nt and amino acid (aa) level, respectively, whereas the overall sequence identity between ThWSV and its closest relative was 69% and 71% at the nt and aa level, respectively.
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Khanal V, Ali A. High Mutation Frequency and Significant Population Differentiation in Papaya Ringspot Virus-W Isolates. Pathogens 2021; 10:pathogens10101278. [PMID: 34684227 PMCID: PMC8537659 DOI: 10.3390/pathogens10101278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/18/2022] Open
Abstract
A total of 101 papaya ringspot virus-W (PRSV-W) isolates were collected from five different cucurbit hosts in six counties of Oklahoma during the 2016–2018 growing seasons. The coat protein (CP) coding region of these isolates was amplified by reverse transcription-polymerase chain reaction, and 370 clones (3–5 clones/isolate) were sequenced. Phylogenetic analysis revealed three phylogroups while host, location, and collection time of isolates had minimal impact on grouping pattern. When CP gene sequences of these isolates were compared with sequences of published PRSV isolates (both P and W strains), they clustered into four phylogroups based on geographical location. Oklahoman PRSV-W isolates formed one of the four distinct major phylogroups. The permutation-based tests, including Ks, Ks *, Z *, Snn, and neutrality tests, indicated significant genetic differentiation and polymorphisms among PRSV-W populations in Oklahoma. The selection analysis confirmed that the CP gene is undergoing purifying selection. The mutation frequencies among all PRSV-W isolates were within the range of 1 × 10−3. The substitution mutations in 370 clones of PRSV-W isolates showed a high proportion of transition mutations, which gave rise to higher GC content. The N-terminal region of the CP gene mostly contained the variable sites with numerous mutational hotspots, while the core region was highly conserved.
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Al-Jaberi MS, Moradi Z, Mehrvar M, Al-Inizi HR, Zakiaghl M. Whole genome characterization of wisteria vein mosaic virus from Iran and its relationship to other members of bean common mosaic virus group. 3 Biotech 2021; 11:407. [PMID: 34471590 DOI: 10.1007/s13205-021-02957-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 08/04/2021] [Indexed: 10/20/2022] Open
Abstract
To date, the complete genome of two wisteria vein mosaic virus (WVMV) has been sequenced worldwide. Here, the genomic sequence of WVMV isolated from Wisteria sinensis in Iran was determined for the first time, using deep RNA sequencing and RT-PCR followed by Sanger sequencing. The sequence was 9694 nucleotides in length; excluding the 3'-poly(A) tail and contained a single open reading frame of 9279 nucleotides encoding a large polyprotein of 3092 amino acids and predicted molecular weight of 35,368 KDa. The genome contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. Sequence analysis suggested that WVMV-Ir sequence shared 76.37-86.01% nucleotide (nt) identity and 82.45-91.91% amino acid (aa) identity with two other isolates (Beijing and JEBU-p) available in the GenBank, the highest with the Chinese isolate Beijing (86.01% nt identity, 91.91% aa identity). Sequence identities over most of the genome were within the range 80-86% and 85-95% at the nt and aa levels, respectively; however, high variability was observed in the 5'-UTR (51.62%), P1 (62.03% nt identity, 50.78% aa identity) and P3 (79.82%nt identity, 78.67% aa identity) regions, suggesting that Ir, Beijing, and JEBU-p are three different strains. These variabilities may be due to different mutation phenomena of a common ancestor virus or mutations caused by different selection pressures in different agro-ecological regions. The results of the phylogenetic analysis indicated that WVMV was most closely related to soybean mosaic virus and watermelon mosaic virus and less closely related to the zantedeschia mild mosaic virus and dasheen mosaic virus. In the greenhouse, WVMV-Ir caused severe symptoms in Phaseolus vulgaris, Vicia faba, W. sinensis, Chenopodium quinoa, C. amaranticolor, and Nicotiana benthamiana. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02957-8.
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Identification and full genomic sequence of nerine yellow stripe virus. Arch Virol 2020; 165:2967-2971. [PMID: 32886214 DOI: 10.1007/s00705-020-04776-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
This study reports the first complete genome sequence of nerine yellow stripe virus (NeYSV, GenBank MT396083). The genome consists of 10,165 nucleotides, excluding the 3'-terminal poly(A) tail. A single open reading frame encodes a large polyprotein of 3294 amino acids with typical potyvirus features. The nuclear inclusion b and coat protein region shares 95% identity with a previously reported partial NeYSV sequence (NC_043153.1). Phylogenetic analysis of the polyprotein amino acid sequence showed that NeYSV clustered with hippeastrum mosaic virus (HiMV YP_006382256.1).
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Igori D, Lim S, Kwon SY, Cho HS, Park JM, Kim HS, Lee HJ, Lee SH, Moon JS. Complete genome sequence and genome organization of achyranthes virus A, a novel member of the genus Potyvirus. Arch Virol 2020; 165:2695-2698. [PMID: 32845374 DOI: 10.1007/s00705-020-04778-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/17/2020] [Indexed: 01/21/2023]
Abstract
The complete genomic sequence of achyranthes virus A (AcVA), from an Achyranthes bidentata Blume plant in South Korea, was determined. The genomic RNA has 9491 nucleotides (nt), excluding the 3'-terminal poly(A) tail and contains an open reading frame typical of members of the genus Potyvirus, family Potyviridae, encoding a large putative polyprotein of 3103 amino acids (aa). Pairwise comparisons showed that the AcVA sequence shares 47.81-57.78% nt sequence identity at the complete genome level, 41.89-56.41% aa sequence identity at the polyprotein level, and 50-63.8% aa sequence identity at the coat protein level with other members of genus Potyvirus. These pairwise comparison values are below the species demarcation cutoff for the family Potyviridae. Our results therefore suggest that this virus should be regarded as a novel member of the genus Potyvirus, tentatively named "achyranthes virus A".
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Affiliation(s)
- Davaajargal Igori
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Seungmo Lim
- Department of Plant Quarantine, Animal and Plant Quarantine Agency, Plant Quarantine Research Center, Gimcheon, 39660, Republic of Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
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Chen L, Anane RF, Wang Z, Yang L, Chen Z, Wen G, Zhao M. Whole-genome sequence analysis of paris virus 1: a novel member of the genus Potyvirus infecting Paris polyphylla var. yunnanensis. Arch Virol 2020; 165:985-988. [DOI: 10.1007/s00705-020-04560-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 01/27/2020] [Indexed: 10/24/2022]
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The RNA-Dependent RNA Polymerase NIb of Potyviruses Plays Multifunctional, Contrasting Roles during Viral Infection. Viruses 2020; 12:v12010077. [PMID: 31936267 PMCID: PMC7019339 DOI: 10.3390/v12010077] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
Potyviruses represent the largest group of known plant RNA viruses and include many agriculturally important viruses, such as Plum pox virus, Soybean mosaic virus, Turnip mosaic virus, and Potato virus Y. Potyviruses adopt polyprotein processing as their genome expression strategy. Among the 11 known viral proteins, the nuclear inclusion protein b (NIb) is the RNA-dependent RNA polymerase responsible for viral genome replication. Beyond its principal role as an RNA replicase, NIb has been shown to play key roles in diverse virus–host interactions. NIb recruits several host proteins into the viral replication complexes (VRCs), which are essential for the formation of functional VRCs for virus multiplication, and interacts with the sumoylation pathway proteins to suppress NPR1-mediated immunity response. On the other hand, NIb serves as a target of selective autophagy as well as an elicitor of effector-triggered immunity, resulting in attenuated virus infection. These contrasting roles of NIb provide an excellent example of the complex co-evolutionary arms race between plant hosts and potyviruses. This review highlights the current knowledge about the multifunctional roles of NIb in potyvirus infection, and discusses future research directions.
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Lan P, He P, Zhang Y, Zhang S, Zhang Z, Chen X, Tan S, Luo H, Cao M, Li F. Molecular characterization of a novel potyvirus infecting noni. Arch Virol 2019; 164:3099-3102. [PMID: 31520219 DOI: 10.1007/s00705-019-04400-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022]
Abstract
The complete genomic sequence of a novel potyvirus from a noni plant in China (Morinda citrifolia) with foliar mosaic and chlorotic symptoms was determined. The genomic RNA consists of 9645 nucleotides (nt) excluding the poly(A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a large putative polyprotein of 3077 amino acids (aa). Pairwise comparisons showed that the virus shares 48.8%-58.5% sequence identity at the genome sequence level, and 38.5%-53.4% identity at the polyprotein sequence level with other members of the genus Potyvirus. Phylogenetic analysis indicated that the virus is most closely related to jasmine virus T and plum pox virus in the genus Potyvirus. These results suggest that this virus should be considered a distinct member of the genus Potyvirus, and it was tentatively named "noni mosaic virus" (NoMV).
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Affiliation(s)
- Pingxiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Yongke Zhang
- Yunnan Institute of Tropical Crops, Jinghong, 666100, China
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Zubing Zhang
- Yunnan Institute of Tropical Crops, Jinghong, 666100, China
| | - Xiaojiao Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Songtao Tan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Hengming Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
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Worrall EA, Bravo-Cazar A, Nilon AT, Fletcher SJ, Robinson KE, Carr JP, Mitter N. Exogenous Application of RNAi-Inducing Double-Stranded RNA Inhibits Aphid-Mediated Transmission of a Plant Virus. FRONTIERS IN PLANT SCIENCE 2019; 10:265. [PMID: 30930914 PMCID: PMC6429036 DOI: 10.3389/fpls.2019.00265] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/19/2019] [Indexed: 05/19/2023]
Abstract
Plant viruses are difficult to control, and they decrease both the quality and yield of crops, thus threatening global food security. A new approach that uses topical application of double-stranded RNA (dsRNA) to induce antiviral RNA-interference has been shown to be effective at preventing virus infection in a range of plants following mechanical inoculation. In this study, topical application of dsRNA was effective against mechanical inoculation and aphid-mediated inoculation with the potyvirus bean common mosaic virus (BCMV). Topical application of dsRNAs targeting either the coding region of the potyviral nuclear inclusion b (NIb) protein (BCMVNIb-dsRNA) or the coat protein (CP) coding region (BCMVCP-dsRNA) protected Nicotiana benthamiana and cowpea (Vigna unguiculata) plants against mechanical inoculation with BCMV. BCMVCP-dsRNA was selected for subsequent aphid transmission experiments. BCMVCP-dsRNA was loaded onto layered double hydroxide nanoparticles to form BCMVCP-BioClay which is a more stable formulation for delivering dsRNA than naked dsRNA. BCMVCP-BioClay was shown to be successful in protecting plants against BCMV transmission by the aphid Myzus persicae. Spraying detached N. benthamiana leaves with BCMVCP-BioClay 5 days prior to exposure to viruliferous aphids protected the leaves from infection by BCMV. Importantly, spraying of intact N. benthamiana and cowpea plants with BCMVCP-BioClay 5 days prior to exposure to viruliferous aphids protected plants of both species from BCMV infection. This study demonstrates that topical application of dsRNA using BioClay protects plants from aphid-mediated virus transmission, which is an important first step toward developing practical application of this approach in crop protection.
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Affiliation(s)
- Elizabeth A. Worrall
- Centre of Horticultural Science, Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Ana Bravo-Cazar
- Department of Plant Sciences, Cambridge University, Cambridge, United Kingdom
| | - Alexander T. Nilon
- Centre of Horticultural Science, Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen J. Fletcher
- Centre of Horticultural Science, Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Karl E. Robinson
- Centre of Horticultural Science, Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - John P. Carr
- Department of Plant Sciences, Cambridge University, Cambridge, United Kingdom
- *Correspondence: Neena Mitter,
| | - Neena Mitter
- Centre of Horticultural Science, Queensland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Neena Mitter,
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