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Xu T, Yang X, Feng X, Luo H, Luo C, Jia MA, Lei L. Sensitive and Visual Detection of Brassica Yellows Virus Using Reverse Transcription Loop-Mediated Isothermal Amplification-Coupled CRISPR-Cas12 Assay. PHYTOPATHOLOGY 2024; 114:474-483. [PMID: 37589413 DOI: 10.1094/phyto-06-23-0195-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Brassica yellows virus (BrYV) is an economically important virus on cruciferous species. In this study, a one-pot reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system was developed for the detection of BrYV. The limit of detection of this method reached 32.8 copies of the BrYV ORF5, which is 100-fold more sensitive than the RT-LAMP method. Moreover, there was no cross-reactivity with other rapeseed-infecting RNA viruses or poleroviruses. We dried the CRISPR/Cas12a reagent in a trehalose and pullulan mixture to retain its efficacy at the RT-LAMP temperature of 63°C in order to allow portable BrYV detection in a water bath. The entire process can be performed in about 1 h, and a positive result can be rapidly and conveniently detected using a handheld UV lamp. In the field, the RT-LAMP-CRISPR/Cas12a assay was accurate and had higher sensitivity than RT-LAMP and reverse transcription-polymerase chain reaction assays. The novel RT-LAMP-CRISPR/Cas12a assay allows convenient, portable, rapid, low-cost, highly sensitive, and specific detection of BrYV and has great potential for on-site monitoring of BrYV.
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Affiliation(s)
- Tengzhi Xu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xiaolan Yang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xia Feng
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Hao Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Chun Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Meng-Ao Jia
- Guizhou Academy of Tobacco Sciences, Guiyang, Guizhou 550001, China
| | - Lei Lei
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
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Jin W, Zhang Y, Su X, Xie Z, Wang R, Du Z, Wang Y, Qiu Y. Genetic diversity analysis of lychnis mottle virus and first identification of Angelica sinensis infection. Heliyon 2023; 9:e17006. [PMID: 37332943 PMCID: PMC10272471 DOI: 10.1016/j.heliyon.2023.e17006] [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: 08/27/2022] [Revised: 04/13/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023] Open
Abstract
Gansu Province is a district renowned for the cultivation of Angelica sinensis (Oliv.) Diels, accounting for greater than 90% of China's total annual production. However, virus infection has caused a reduction in A. sinensis yield. Here, we collected suspected virus-infected A. sinensis leaf samples from Gansu Province's A. sinensis cultivation area. For the first time, using small RNA deep sequencing and RT-PCR, lychnis mottle virus (LycMoV) was found to naturally infect A. sinensis. The coat protein (cp) gene of the Gansu A. sinensis LycMoV isolate was obtained through cloning, where its nucleotide and amino acid identity was highest while having the closest affinity to the China Pearl (i.e., Prunus persica) isolate. Recombination analysis indicated that genetic recombination had only a limited influencing effect on the molecular evolution of LycMoV. Moreover, results from genetic diversity analysis indicated that the host, geographic isolation, and genetic drift may be the main factors that contributed to the formation of genetic diversity and differentiation in LycMoV. Furthermore, the LycMoV population trend was expansionary. Selection pressure may also be the main driver for the evolution of the entire LycMoV population, while the driving effect of genetic recombination is limited. This study marks a new LycMoV host (i.e., A. sinensis) for the first time and provides scientific support for the identification, prevention, and control of LycMoV.
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Affiliation(s)
- Weijie Jin
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
| | - Yubao Zhang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
| | - Xuesi Su
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
| | - Zhongkui Xie
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
| | - Ruoyu Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
| | - Zhongpei Du
- Jiuquan Vocational and Technical College, Jiuquan, 735000, China
| | - Yajun Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
| | - Yang Qiu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Lanzhou, 730000, China
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Peng Q, Li W, Zhou X, Sun C, Hou Y, Hu M, Fu S, Zhang J, Kundu JK, Lei L. Genetic Diversity Analysis of Brassica Yellows Virus Causing Aberrant Color Symptoms in Oilseed Rape. PLANTS (BASEL, SWITZERLAND) 2023; 12:1008. [PMID: 36903869 PMCID: PMC10005696 DOI: 10.3390/plants12051008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The emergence of brassica yellow virus (BrYV) has increasingly damaged crucifer crops in China in recent years. In 2020, a large number of oilseed rape in Jiangsu showed aberrant leaf color. A combined RNA-seq and RT-PCR analysis identified BrYV as the major viral pathogen. A subsequent field survey showed that the average incidence of BrYV was 32.04%. In addition to BrYV, turnip mosaic virus (TuMV) was also frequently detected. As a result, two near full-length BrYV isolates, BrYV-814NJLH and BrYV-NJ13, were cloned. Based on the newly obtained sequences and the reported BrYV and turnip yellow virus (TuYV) isolates, a phylogenetic analysis was performed, and it was found that all BrYV isolates share a common root with TuYV. Pairwise amino acid identity analysis revealed that both P2 and P3 were conserved in BrYV. Additionally, recombination analysis revealed seven recombinant events in BrYV as TuYV. We also attempted to determine BrYV infection by quantitative leaf color index, but no significant correlation was found between the two. Systemic observations indicated that BrYV-infected plants had different symptoms, such as no symptom, purple stem base and red old leaves. Overall, our work proves that BrYV is closely related to TuYV and could be considered as an epidemic strain for oilseed rape in Jiangsu.
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Affiliation(s)
- Qi Peng
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Wei Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaoying Zhou
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Chengming Sun
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yan Hou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
| | - Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Sanxiong Fu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jiban Kumar Kundu
- Plant Virus and Vector Interactions-Centre for Plant Virus Research, Crop Research Institute, Drnovska 507/73, 161 06 Praha, Czech Republic
- Laboratory of Virology-Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague, Czech Republic
| | - Lei Lei
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
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Liu SY, Zuo DP, Zhang ZY, Wang Y, Han CG. Identification and Functional Analyses of Host Proteins Interacting with the P3a Protein of Brassica Yellows Virus. BIOLOGY 2023; 12:biology12020202. [PMID: 36829481 PMCID: PMC9952887 DOI: 10.3390/biology12020202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Viruses are obligate parasites that only undergo genomic replication in their host organisms. ORF3a, a newly identified non-AUG-initiated ORF encoded by members of the genus Polerovirus, is required for long-distance movement in plants. However, its interactions with host proteins still remain unclear. Here, we used Brassica yellows virus (BrYV)-P3a as bait to screen a plant split-ubiquitin-based membrane yeast two-hybrid (MYTH) cDNA library to explain the functional role of P3a in viral infections. In total, 138 genes with annotations were obtained. Bioinformatics analyses revealed that the genes from carbon fixation in photosynthetic, photosynthesis pathways, and MAPK signaling were affected. Furthermore, Arabidopsis thaliana purine permease 14 (AtPUP14), glucosinolate transporter 1 (AtGTR1), and nitrate transporter 1.7 (AtNRT1.7) were verified to interact with P3a in vivo. P3a and these three interacting proteins mainly co-localized in the cytoplasm. Expression levels of AtPUP14, AtGTR1, and AtNRT1.7 were significantly reduced in response to BrYV during the late stages of viral infection. In addition, we characterized the roles of AtPUP14, AtGTR1, and AtNRT1.7 in BrYV infection in A. thaliana using T-DNA insertion mutants, and the pup14, gtr1, and nrt1.7 mutants influenced BrYV infection to different degrees.
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Zhao X, He C, Gao D, Xu T, Li X, Liu J, Li S, Wang H. Construction of Infectious cDNA Clone of Brassica Yellows Virus Isolated from Strawberry and Establishment of TaqMan RT-qPCR. PLANTS (BASEL, SWITZERLAND) 2022; 11:3380. [PMID: 36501425 PMCID: PMC9735513 DOI: 10.3390/plants11233380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The natural host range for brassica yellows virus (BrYV) is generally limited to Cruciferae. However, we found that BrYV can naturally infect strawberry. The full-length genome sequences of BrYV-MB (accession No. MZ666129) and BrYV-HY (accession No. ON060762) identified in strawberry from Yantai and Beijing, China, were obtained by high-throughput sequencing (HTS) combined with the RT-PCR and RACE techniques. The complete genome sequences of BrYV-MB and BrYV-HY are 5666 nt and contain six open reading frames (ORFs). The two isolates have the highest nucleotide (nt) sequence identity of 99.0%. The infectious cDNA clone of BrYV-HY was constructed through homologous recombination and used to agroinfiltrate Nicotiana benthamiana and Arabidopsis thaliana. The inoculated leaves of N. benthamiana showed necrotic symptoms after 4 days of inoculation (dpi), and the systematic leaves of A. thaliana exhibited purple symptoms at 14 dpi. To develop a rapid and high-sensitive method for the detection of BrYV, a TaqMan real-time fluorescence quantitative RT-PCR method (TaqMan RT-qPCR) was established. Under optimum reaction conditions, the sensitivity of the detection was as low as 100 fg and approximately 100-fold more sensitive than the conventional RT-PCR, so it can be used in large-scale testing.
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Affiliation(s)
- Xiaoli Zhao
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chengyong He
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dehang Gao
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Tengfei Xu
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xiaofeng Li
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Junjie Liu
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongqing Wang
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
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Guo Y, Wu W, Zhang X, Ding M, Yu J, Zhang J, Jia MA, Tian Y. Triplex Immunostrip Assay for Rapid Diagnosis of Tobacco Mosaic Virus, Tobacco Vein Banding Mosaic Virus, and Potato Virus Y. PLANT DISEASE 2022; 106:3033-3039. [PMID: 35612580 DOI: 10.1094/pdis-08-21-1756-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mixed virus infection has increasingly become a problem in the production of Solanaceae crops in recent years; therefore, a fast and accurate detection method is needed. In this study, a novel triplex immunostrip assay was developed for the simultaneous detection of tobacco mosaic virus (TMV), tobacco vein banding mosaic virus (TVBMV), and potato virus Y (PVY). The limits of detection of this novel immunostrip reached 200 ppb (ng/ml), 1 ppm (µg/ml), and 2 ppm for TMV, PVY, and TVBMV particles, respectively. Importantly, no cross-reactivity was observed among TMV, TVBMV, and PVY or to a nontarget virus. When the assay was applied to suspected virus-infected tobacco, tomato, and potato samples collected from fields in Southwest China, samples of single or mixed virus infection were successfully identified. In conclusion, the triplex immunostrip assay provides a fast and easy to use on-site detection method for field epidemiological studies of TMV, TVBMV, and PVY, and for managing diseases that are caused by them.
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Affiliation(s)
- Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang-550081, China
| | - Wei Wu
- Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou-350002, China
| | - Xiaolian Zhang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang-550081, China
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang-550081, China
| | - Ming Ding
- Biotechnology and Germplasm Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, China; Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang-550081, China
| | - Jing Yu
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang-550081, China
| | - Jie Zhang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang-550081, China
| | - Meng-Ao Jia
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang-550081, China
| | - Yanping Tian
- Department of Plant Protection, Shandong Agriculture University, Taian-271018, China
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Umar M, Tegg RS, Farooq T, Thangavel T, Wilson CR. Abundance of Poleroviruses within Tasmanian Pea Crops and Surrounding Weeds, and the Genetic Diversity of TuYV Isolates Found. Viruses 2022; 14:1690. [PMID: 36016314 PMCID: PMC9416036 DOI: 10.3390/v14081690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 01/08/2023] Open
Abstract
The genus Polerovirus contains positive-sense, single-stranded RNA plant viruses that cause significant disease in many agricultural crops, including vegetable legumes. This study aimed to identify and determine the abundance of Polerovirus species present within Tasmanian pea crops and surrounding weeds that may act as virus reservoirs. We further sought to examine the genetic diversity of TuYV, the most commonly occurring polerovirus identified. Pea and weed samples were collected during 2019-2020 between October and January from thirty-four sites across three different regions (far northwest, north, and midlands) of Tasmania and tested by RT-PCR assay, with selected samples subject to next-generation sequencing. Results revealed that the presence of polerovirus infection and the prevalence of TuYV in both weeds and pea crops varied across the three Tasmanian cropping regions, with TuYV infection levels in pea crops ranging between 0 and 27.5% of tested plants. Overall, two species members from each genus, Polerovirus and Potyvirus, one member from each of Luteovirus, Potexvirus, and Carlavirus, and an unclassified virus from the family Partitiviridae were also found as a result of NGS data analysis. Analysis of gene sequences of the P0 and P3 genes of Tasmanian TuYV isolates revealed substantial genetic diversity within the collection, with a few isolates appearing more closely aligned with BrYV isolates. Questions remain around the differentiation of TuYV and BrYV species. Phylogenetic inconsistency in the P0 and P3 ORFs supports the concept that recombination may have played a role in TuYV evolution in Tasmania. Results of the evolutionary analysis showed that the selection pressure was higher in the P0 gene than in the P3 gene, and the majority of the codons for each gene are evolving under purifying selection. Future full genome-based analyses of the genetic variations will expand our understanding of the evolutionary patterns existing among TuYV populations in Tasmania.
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Affiliation(s)
- Muhammad Umar
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, Hobart, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, Hobart, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| | - Tahir Farooq
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Tamilarasan Thangavel
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, Hobart, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
- Department of Agriculture and Fisheries (Queensland), Bundaberg Research Facility, 49 Ashfield Road, Bundaberg, QLD 4670, Australia
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, Hobart, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
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Umar M, Farooq T, Tegg RS, Thangavel T, Wilson CR. Genomic Characterisation of an Isolate of Brassica Yellows Virus Associated with Brassica Weed in Tasmania. PLANTS (BASEL, SWITZERLAND) 2022; 11:884. [PMID: 35406863 PMCID: PMC9003488 DOI: 10.3390/plants11070884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Brassica yellows virus (BrYV), a tentative species in the genus Polerovirus, of the Solemoviridae family, is a phloem-restricted and aphid-transmitted virus with at least three genotypes (A, B, and C). It has been found across mainland China, South Korea, and Japan. BrYV was previously undescribed in Tasmania, and its genetic variability in the state remains unknown. Here, we describe a near-complete genome sequence of BrYV (genotype A) isolated from Raphanus raphanistrum in Tasmania using next-generation sequencing and sanger sequencing of RT-PCR products. BrYV-Tas (GenBank Accession no. OM469309) possesses a genome of 5516 nucleotides (nt) and shares higher sequence identity (about 90%) with other BrYV isolates. Phylogenetic analyses showed variability in the clustering patterns of the individual genes of BrYV-Tas. Recombination analysis revealed beginning and ending breakpoints at nucleotide positions 1922 to 5234 nt, with the BrYV isolate LC428359 and BrYV isolate KY310572 identified as major and minor parents, respectively. Results of the evolutionary analysis showed that the majority of the codons for each gene are evolving under purifying selection, though a few codons were also detected to have positive selection pressure. Taken together, our findings will facilitate an understanding of the evolutionary dynamics and genetic diversity of BrYV.
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Affiliation(s)
- Muhammad Umar
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| | - Tahir Farooq
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
| | - Tamilarasan Thangavel
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
- Department of Agriculture and Fisheries (Queensland), Bundaberg Research Facility, 49 Ashfield Road, Bundaberg, QLD 4670, Australia
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia; (M.U.); (R.S.T.); (T.T.)
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Kavalappara SR, Milner H, Riley DG, Bag S. First report of turnip yellows virus infecting cabbage (Brassica oleracea var. capitata) in the USA. PLANT DISEASE 2022; 106:2273. [PMID: 35084946 DOI: 10.1094/pdis-10-21-2174-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
During the spring of 2021, cabbage (Brassica oleracea var. capitata) planted in the research farm at the University of Georgia, Tifton, exhibited leaf distortion, yellow and purple discoloration at the leaf margin of older leaves, and severe stunting. Symptoms were present on nearly 30% of the plants in the field. To identify the potential agents associated, leaf tissues from two symptomatic plants were sent for high throughput sequencing (HTS) of small RNA (sRNA; DNB sequencing, SE read 1x75bp) to Beijing Genomics Institute, China. From each sample, ~ 18 million raw reads were generated. The reads with poor quality and adapter sequences were removed using CLC Genomics Workbench 21.2 (Qiagen, Germantown, MD). Of the total reads, 2,093 and 3,889 reads aligned to the genome of turnip yellows virus (TuYV) in samples one and two, respectively. Reads of turnip mosaic virus (TuMV) were also detected (data not shown). Partial sequences of TuYV assembled from samples one and two showed 89.5% and 89.9% match and 86% and 93% coverage, respectively, with the genome of the type isolate of TuYV (NC_003743) from the United Kingdom. To confirm the presence of TuYV in the samples collected from the same location, specific primers were designed targeting the P0 region (FP- 5'ACAAAAGAAACCAG- GAGGGAATCC3'; RP-5'GCCTTTTCATACAAACATTTCGGTG3') and coat protein (CP) region (FP-5'GTTAATGAATACGGTCGTGGGTAG3'; RP-5'ATTCTGAAAGAACCAGCT- ATCGATG3') of the virus. Eight of 20 (40%) symptomatic samples were determined to be infected with TuYV based on the amplification of expected size products of the P0 (786 nt) and the CP gene (581 nt) in reverse transcription-PCR (RT-PCR). All samples were also tested for the presence of TuMV by RT-PCR as in Sanchez et al. (2003), but none tested positive despite being identified in HTS. Symptoms on samples from which eithervirus could not be detected indicates the involvement of other factors and would require further studies. The partial P0 and CP gene amplicons of TuYV from two samples each were Sanger sequenced bi-directionally at Genewiz (South Plainfield, NJ) and confirmed as TuYV using BLASTn. The partial CP gene sequences from two samples shared 98.7% nucleotide sequence identity with each other and 88.0% (OK349421) and 87.1% (OK349422) identity with the type isolate. The partial P0 gene sequences (OK349423 and OK349424) shared 99.6% nucleotide sequence identity with each other and 92.2% identity with the type isolate. TuYV, formerly known as beet western yellows virus (BWYV) (Mayo, 2002), genus Palerovirus, family Solemoviridae (Walker et al., 2021), is transmitted persistently by aphids (Stevens et al., 2008), and is distributed throughout temperate regions of the world (Kawakubo et al., 2021). TuYV has a wide host range, including brassica, vegetables and weeds (Stevens et al., 2008). However, losses have been reported primarily on canola (B. napus) in Australia (Jones, 2007) and Europe (Stevens et al., 2008). On cabbage, TuYV infections have been reported from China (Zhang et al., 2016), Serbia (Milošević et al., 2020) and the Philippines (Buxton-Kirk et al, 2020). TuYV (BWYV) has been found infecting shepherd's purse (Capsella bursa-pastoris) in California (Falk and Duffus, 1984), but there are no reports of the virus from any cultivated crops in the USA. To our knowledge, this is the first report of TuYV in cabbage in the USA. More studies are needed to understand its occurrence and impact on cabbage crops in Georgia as well as other regions in the USA.
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Affiliation(s)
- Saritha Raman Kavalappara
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Department of Plant Pathology, Tifton, Georgia, United States;
| | - Hayley Milner
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Department of Plant Pathology, Tifton, Georgia, United States;
| | - David G Riley
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Entomology, Tifton, Georgia, United States;
| | - Sudeep Bag
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Plant Pathology, Tifton, Georgia, United States;
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Abstract
Amplification of different nucleic acid targets in the same reaction (multiplex polymerase chain reaction) is challenging but an extremely useful tool especially for viroid diagnosis. In the amplification mixtures, several pairs of primers work together in the same conditions to detect different targets. Here, we describe the development and use of a multiplex reverse transcription polymerase chain reaction protocol highlighting the most crucial factors that can significantly affect the quality of the method. First, particular attention must be paid to primer design. Then, the amplification mixture and temperature conditions must be calibrated precisely to avoid cross reactivity or loss in sensitivity. Finally, the detection system of the amplification results must allow a specific identification of the amplified target(s).
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Affiliation(s)
- Francesco Faggioli
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia agraria (CREA)-Centro di Ricerca Difesa e Certificazione (CREA-DC), Rome, Italy.
| | - Marta Luigi
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia agraria (CREA)-Centro di Ricerca Difesa e Certificazione (CREA-DC), Rome, Italy
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11
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A Simple Method for the Acquisition and Transmission of Brassica Yellows Virus from Transgenic Plants and Frozen Infected Leaves by Aphids. PLANTS 2021; 10:plants10091944. [PMID: 34579476 PMCID: PMC8471377 DOI: 10.3390/plants10091944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022]
Abstract
Brassica yellows virus (BrYV) is a tentative species of the genus Polerovirus, which occurs widely, and mostly damages Brassicaceae plants in East Asia. Because BrYV cannot be transmitted mechanically, an insect-based transmission method is required for further virus research. Here, a reliable and unrestricted method is described, in which non-viruliferous aphids (Myzus persicae) acquired BrYV from transgenic Arabidopsis thaliana, harboring the full-length viral genome germinated from seeds and its frozen leaves. The aphids then transmitted the virus to healthy plants. There was no significant difference in acquisition rates between fresh and frozen infected leaves, although the transmission rate from frozen infected leaves was lower compared to fresh infected leaves. This simple novel method may be used to preserve viral inocula, evaluate host varietal resistance to BrYV, and investigate interactions among BrYV, aphids, and hosts.
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12
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Maurastoni M, Sá-Antunes TF, Oliveira SA, Santos AMC, Ventura JA, Fernandes PMB. A multiplex RT-PCR method to detect papaya meleira virus complex in adult pre-flowering plants. Arch Virol 2020; 165:1211-1214. [PMID: 32170392 DOI: 10.1007/s00705-020-04588-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022]
Abstract
Papaya sticky disease (PSD), which can destroy orchards, was first attributed to papaya meleira virus (PMeV). However, the discovery of papaya meleira virus 2 (PMeV2) associated with PSD plants impose the need to detect this viral complex. We developed a multiplex RT-PCR (mPCR) technique capable of detecting two viruses in a single assay from pre-flowering plant samples, which is a useful tool for early diagnosis of PSD. We also determined the limit of detection (LOD) using asymmetric plasmid dilutions of both PMeV and PMeV2, which revealed that a higher titer of one virus prevents detection of the other. Thus, this technique is an alternative method for detecting PMeV and PMeV2 in a single reaction.
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Affiliation(s)
- Marlonni Maurastoni
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Tathiana F Sá-Antunes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Scarlett A Oliveira
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Alexandre M C Santos
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - José A Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória, Epírito Santo, Brazil
| | - Patricia M B Fernandes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil.
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13
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Sevik MA. Viruses infecting cool season crops in the northern Turkey. AN ACAD BRAS CIENC 2019; 91:e20180224. [PMID: 31365647 DOI: 10.1590/0001-3765201920180224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/15/2018] [Indexed: 11/22/2022] Open
Abstract
Virus diseases of cool season vegetable crops (mainly cabbage, white and red head cabbage, broccoli, kale, radish, rocket salad, garden cress, and turnip) were surveyed in Bafra Plain, Turkey during winter 2017, and 2018. Leaf samples were collected from different species of the Brassicaceae family showing mosaic, mottling, necrotic spots, malformation, and chlorosis symptoms. These samples were tested for the presence of Cauliflower mosaic virus (CaMV), Cucumber mosaic virus (CMV), Beet western yellows virus (BWYV), Radish mosaic virus (RaMV), Turnip mosaic virus (TuMV), Turnip yellow mosaic virus (TYMV), and Turnip yellows virus (TuYV) by biological and serological methods. A total of 455 samples were collected from cole crop fields and tested for the seven viruses by double-antibody sandwich ELISA using specific polyclonal antibodies. According to the results, out of these, 7 % of the samples were infected by at least one of these viruses. TuMV was the most prevalent virus detected in cole crops. TuMV, CaMV, and CMV were detected in 3 %, 2 %, and 2 % of infected samples, respectively, and the infection rate of these three viruses changed significantly among Brassica species.
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Affiliation(s)
- Mehmet A Sevik
- Department of Plant Protection, Faculty of Agriculture, University of Ondokuz Mayis, 55139, Atakum, Samsun, Turkey
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14
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Wang Q, Xu FZ, An LL, Xiang HY, Zhang WH, Liu GS, Liu HB. Molecular characterization of a new recombinant brassica yellows virus infecting tobacco in China. Virus Genes 2019; 55:253-256. [PMID: 30697673 DOI: 10.1007/s11262-019-01636-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/07/2019] [Indexed: 10/27/2022]
Abstract
Brassica yellows virus (BrYV), prevalently distributed throughout mainland China and South Korea while triggering serious diseases in cruciferous crops, is proposed to be a new species in the genus Polerovirus within the family Luteoviridae. There are three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) reported in cabbage and radish. Here, we describe a new BrYV isolate infecting tobacco plants in the field, which was named BrYV-NtabQJ. The complete genome sequence of BrYV-NtabQJ is 5741 nt in length, and 89% of the sequence shares higher sequence identities (about 90%) with different BrYV isolates. However, it possesses a quite divergent region within ORF5, which is more close to Beet western yellows virus (BWYV), Beet mild yellowing virus (BMYV) and Beet chlorosis virus (BChV). A significant recombination event was then detected among BrYV-NtabQJ, BrYV-B Beijng isolate (BrYV-BBJ) and BWYV Leonurus sibiricus isolate (BWYV-LS). It is proposed that BrYV-NtabQJ might be an interspecific recombinant between BrYV-BBJ and BWYV-LS, and the recombination might result in the successful aphid transmission of BrYV from cruciferous crops to tobacco. And it also poses new challenges for BrYV diagnosis and the vegetable production.
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Affiliation(s)
- Qian Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Fang-Zheng Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Lu-Lu An
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Hai-Ying Xiang
- Yunnan Academy of Tobacco Science, Kunming, 650106, People's Republic of China
| | - Wei-Hua Zhang
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural Sciences, Ji'nan, 250100, People's Republic of China
| | - Guan-Shan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China.
| | - Hao-Bao Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China.
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