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Adegbola RO, Ponvert ND, Brown JK. Genetic Variability Among U.S.-Sentinel Cotton Plot Cotton Leafroll Dwarf Virus and Globally Available Reference Isolates Based on ORF0 Diversity. PLANT DISEASE 2024; 108:1799-1811. [PMID: 38277653 DOI: 10.1094/pdis-02-23-0243-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: 01/28/2024]
Abstract
The aphid-transmitted polerovirus, cotton leafroll dwarf virus (CLRDV), first characterized from symptomatic cotton plants in South America, has been identified in commercial cotton plantings in the United States. Here, the CLRDV intraspecific diversity was investigated by comparative sequence analysis of the most divergent CLRDV coding region, ORF0/P0. Bayesian analysis of ORF0 sequences for U.S. and reference populations resolved three well-supported sister clades comprising one U.S. and two South American lineages. Principal component analysis (PCA) identified seven statistically supported intraspecific populations. The Bayesian phylogeny and PCA dendrogram-inferred relationships were congruent. Population analysis of ORF0 sequences indicated most lineages have evolved under negative selection, albeit certain sites/isolates evolved under positive selection. Both U.S. and South American isolates exhibited extensive ORF0 diversity. At least two U.S. invasion foci were associated with their founder populations in Alabama-Georgia and eastern Texas. The Alabama-Georgia founder is implicated as the source of recent widespread expansion and establishment of secondary disease foci throughout the southeastern-central United States. Based on the geographically restricted distribution, spread of another extant Texas population appeared impeded by a population bottleneck. Extant CLRDV isolates represent several putative introductions potentially associated with catastrophic weather events dispersing viruliferous cotton aphids of unknown origin(s).
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Affiliation(s)
| | | | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721
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Pimenta RJG, Macleod K, Babb R, Coleman K, MacDonald J, Asare-Bediako E, Newbert MJ, Jenner CE, Walsh JA. Genetic Variation of Turnip Yellows Virus in Arable and Vegetable Brassica Crops, Perennial Wild Brassicas, and Aphid Vectors Collected from the Plants. PLANT DISEASE 2024; 108:616-623. [PMID: 37787684 DOI: 10.1094/pdis-05-23-0906-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: 10/04/2023]
Abstract
Turnip yellows virus (TuYV; Polerovirus, Solemoviridae) infects and causes yield losses in a range of economically important crop species, particularly the Brassicaceae. It is persistently transmitted by several aphid species and is difficult to control. Although the incidence and genetic diversity of TuYV has been extensively investigated in recent years, little is known about how the diversity within host plants relates to that in its vectors. Arable oilseed rape (Brassica napus) and vegetable brassica plants (Brassica oleracea), wild cabbage (B. oleracea), and aphids present on these plants were sampled in the field in three regions of the United Kingdom. High levels of TuYV (82 to 97%) were detected in plants in all three regions following enzyme-linked immunosorbent assays. TuYV was detected by reverse transcription polymerase chain reaction in Brevicoryne brassicae aphids collected from plants, and TuYV sequences were obtained. Two TuYV open reading frames, ORF0 and ORF3, were partially sequenced from 15 plants, and from one aphid collected from each plant. Comparative analyses between TuYV sequences from host plants and B. brassicae collected from respective plants revealed differences between some ORF0 sequences, which possibly indicated that at least two of the aphids might not have been carrying the same TuYV isolates as those present in their host plants. Maximum likelihood phylogenetic analyses including published, the new TuYV sequences described above, 101 previously unpublished sequences of TuYV from oilseed rape in the United Kingdom, and 13 also previously unpublished sequences of TuYV from oilseed rape in Europe and China revealed three distinct major clades for ORF0 and one for ORF3, with some distinct subclades. Some clustering was related to geographic origin. Explanations for TuYV sequence differences between plants and the aphids present on respective plants and implications for the epidemiology and control of TuYV are discussed.
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Affiliation(s)
- Ricardo J G Pimenta
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
- Centre for Molecular Biology and Genetic Engineering, University of Campinas, 13083-875, Campinas, Brazil
| | - Kyle Macleod
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
| | - Robyn Babb
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
| | - Kaitlyn Coleman
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
| | - Joni MacDonald
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
| | - Elvis Asare-Bediako
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
- University of Energy and Natural Resources, Sunyani, Ghana
| | - Max J Newbert
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
| | - Carol E Jenner
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
| | - John A Walsh
- School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, U.K
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Wylie S, Habili N. State-of-the-Art Plant Virus Research in Australasia. Viruses 2023; 15:1311. [PMID: 37376611 DOI: 10.3390/v15061311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The Special Issue 'State-of-the-Art Plant Virus Research in Australasia' in Viruses provided a fascinating snapshot of plant and fungus virus research being undertaken in Australasia during the final year of the official COVID-19 pandemic [...].
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Affiliation(s)
- Steve Wylie
- The Harry Butler Institute, Murdoch University, 90 South Street, Perth, WA 6150, Australia
| | - Nuredin Habili
- The Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove, Urrbrae, SA 5064, Australia
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia
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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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Farooq T, Hussain MD, Shakeel MT, Riaz H, Waheed U, Siddique M, Shahzadi I, Aslam MN, Tang Y, She X, He Z. Global genetic diversity and evolutionary patterns among Potato leafroll virus populations. Front Microbiol 2022; 13:1022016. [PMID: 36590416 PMCID: PMC9801716 DOI: 10.3389/fmicb.2022.1022016] [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: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 01/04/2023] Open
Abstract
Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world.
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Affiliation(s)
- Tahir Farooq
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Muhammad Dilshad Hussain
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Muhammad Taimoor Shakeel
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hasan Riaz
- Institute of Plant Protection, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Ummara Waheed
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Maria Siddique
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Irum Shahzadi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Muhammad Naveed Aslam
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yafei Tang
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Xiaoman She
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
| | - Zifu He
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
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