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Abrahamian P, Tian T, Posis K, Guo Y, Yu D, Blomquist CL, Wei G, Adducci B, Vidalakis G, Bodaghi S, Osman F, Roy A, Nunziata SO, Nakhla M, Mavrodieva V, Rivera Y. Genetic Analysis of the Emerging Citrus Yellow Vein Clearing Virus Reveals a Divergent Virus Population in American Isolates. PLANT DISEASE 2024; 108:1544-1554. [PMID: 38127632 DOI: 10.1094/pdis-09-23-1963-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: 12/23/2023]
Abstract
Citrus yellow vein clearing virus is a previously reported citrus virus from Asia with widespread distribution in China. In 2022, the California Department of Food and Agriculture conducted a multipest citrus survey targeting multiple citrus pathogens including citrus yellow vein clearing virus (CYVCV). In March 2022, a lemon tree with symptoms of vein clearing, chlorosis, and mottling in a private garden in the city of Tulare, California, tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and noncitrus species, were collected and tested for CYVCV using conventional reverse transcription polymerase chain reaction, reverse transcription quantitative polymerase chain reaction, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using 17 complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study made up the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, the CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area.
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Affiliation(s)
- Peter Abrahamian
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Tongyan Tian
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Katie Posis
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Ying Guo
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Doris Yu
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Cheryl L Blomquist
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Gang Wei
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Benjamin Adducci
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Avijit Roy
- Molecular Plant Pathology Laboratory, Beltsville Agriculture Research Center, USDA-ARS, Beltsville, MD 20705
| | - Schyler O Nunziata
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Mark Nakhla
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Vessela Mavrodieva
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Yazmín Rivera
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
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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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Mehdi F, Cao Z, Zhang S, Gan Y, Cai W, Peng L, Wu Y, Wang W, Yang B. Factors affecting the production of sugarcane yield and sucrose accumulation: suggested potential biological solutions. FRONTIERS IN PLANT SCIENCE 2024; 15:1374228. [PMID: 38803599 PMCID: PMC11128568 DOI: 10.3389/fpls.2024.1374228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024]
Abstract
Environmental stresses are the main constraints on agricultural productivity and food security worldwide. This issue is worsened by abrupt and severe changes in global climate. The formation of sugarcane yield and the accumulation of sucrose are significantly influenced by biotic and abiotic stresses. Understanding the biochemical, physiological, and environmental phenomena associated with these stresses is essential to increase crop production. This review explores the effect of environmental factors on sucrose content and sugarcane yield and highlights the negative effects of insufficient water supply, temperature fluctuations, insect pests, and diseases. This article also explains the mechanism of reactive oxygen species (ROS), the role of different metabolites under environmental stresses, and highlights the function of environmental stress-related resistance genes in sugarcane. This review further discusses sugarcane crop improvement approaches, with a focus on endophytic mechanism and consortium endophyte application in sugarcane plants. Endophytes are vital in plant defense; they produce bioactive molecules that act as biocontrol agents to enhance plant immune systems and modify environmental responses through interaction with plants. This review provides an overview of internal mechanisms to enhance sugarcane plant growth and environmental resistance and offers new ideas for improving sugarcane plant fitness and crop productivity.
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Affiliation(s)
- Faisal Mehdi
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Zhengying Cao
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Shuzhen Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Yimei Gan
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Wenwei Cai
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Lishun Peng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Yuanli Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Wenzhi Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Benpeng Yang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
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Ohlson EW, Khatri N, Wilson JR. Experimental Host and Vector Ranges of the Emerging Maize Yellow Mosaic Polerovirus. PLANT DISEASE 2024; 108:1246-1251. [PMID: 37923977 DOI: 10.1094/pdis-06-23-1124-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: 11/06/2023]
Abstract
Maize yellow mosaic virus (MaYMV) is an emerging polerovirus that has been detected in maize, other cereal crops, and weedy grass species in Asia, Africa, and the Americas. Disease symptoms in maize include prominent leaf tip reddening and stunting. Infection by MaYMV has been reported to reduce plant growth and yields by 10 to 30% in some instances. In this study, an experimental host range for MaYMV among agronomically important cereal crops and common grasses was established. Additional aphid species were assessed as potential vectors for MaYMV, and their transmission efficiencies were determined. Here, we report oats, foxtail millet, barley, and rye as new experimental cereal crop hosts of MaYMV in addition to confirming the previously reported hosts of corn, sorghum, wheat, and broom millet. Four of the nine other grass species evaluated were also identified as suitable experimental hosts for MaYMV: ryegrass, switchgrass, green foxtail, and sand love grass. Interestingly, no visible symptoms were present in any of the infected hosts besides the susceptible maize control. Vector range studies identified the greenbug aphid Schizaphis graminum as a new vector of MaYMV, though transmission efficiency was lower than the previously reported Rhopalosiphum maidis vector and similar to the other known aphid vector R. padi. Given MaYMV's global ubiquity, ability to evade detection, and broad host range, further characterization of yield impacts and identification of viable control strategies are desirable.
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Affiliation(s)
- Erik W Ohlson
- Corn, Soybean, and Wheat Quality Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Wooster, OH 44691
| | - Nitika Khatri
- Corn, Soybean, and Wheat Quality Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Wooster, OH 44691
| | - Jennifer R Wilson
- Corn, Soybean, and Wheat Quality Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Wooster, OH 44691
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Xu HM, He EQ, Yang ZL, Bi ZW, Bao WQ, Sun SR, Lu JJ, Gao SJ. Phylogeny and Genetic Divergence among Sorghum Mosaic Virus Isolates Infecting Sugarcane. PLANTS (BASEL, SWITZERLAND) 2023; 12:3759. [PMID: 37960115 PMCID: PMC10648118 DOI: 10.3390/plants12213759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Sorghum mosaic virus (SrMV, the genus Potyvirus of the family Potyviridae) is a causal agent of common mosaic in sugarcane and poses a threat to the global sugar industry. In this study, a total of 901 sugarcane leaf samples with mosaic symptom were collected from eight provinces in China and were detected via RT-PCR using a primer pair specific to the SrMV coat protein (CP). These leaf samples included 839 samples from modern cultivars (Saccharum spp. hybrids) and 62 samples from chewing cane (S. officinarum). Among these, 632 out of 901 (70.1%) samples were tested positive for SrMV. The incidences of SrMV infection were 72.3% and 40.3% in modern cultivars and chewing cane, respectively. Phylogenetic analysis showed that all tested SrMV isolates were clustered into three clades consisting of six phylogenetic groups based on 306 CP sequences (this study = 265 and GenBank database = 41). A total of 10 SrMV isolates from South America (the United States and Argentina) along with 106 isolates from China were clustered in group D, while the remaining 190 SrMV isolates from Asia (China and Vietnam) were dispersed in five groups. The SrMV isolates in group F were limited to Yunnan province in China, and those in group A were spread over eight provinces. A significant genetic heterogeneity was elucidated in the nucleotide sequence identities of all SrMV CPs, ranging from 69.0% to 100%. A potential recombination event was postulated among SrMV isolates based on CP sequences. All tested SrMV CPs underwent dominant negative selection. Geographical isolation (South America vs. Asia) and host types (modern cultivars vs. chewing cane) are important factors promoting the genetic differentiation of SrMV populations. Overall, this study contributes to the global understanding of the genetic evolution of SrMV and provides a valuable resource for the epidemiology and management of the mosaic in sugarcane.
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Affiliation(s)
- Hui-Mei Xu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.-M.X.); (Z.-W.B.); (W.-Q.B.)
| | - Er-Qi He
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi 562400, China;
| | - Zu-Li Yang
- Laibin Academy of Agricultural Sciences, Laibin 546100, China;
| | - Zheng-Wang Bi
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.-M.X.); (Z.-W.B.); (W.-Q.B.)
| | - Wen-Qing Bao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.-M.X.); (Z.-W.B.); (W.-Q.B.)
| | - Sheng-Ren Sun
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China;
| | - Jia-Ju Lu
- Guizhou Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi 562400, China;
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.-M.X.); (Z.-W.B.); (W.-Q.B.)
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Dou R, Huang Q, Hu T, Yu F, Hu H, Wang Y, Zhou X, Qian Y. Molecular Variation and Genomic Function of Citrus Vein Enation Virus. Int J Mol Sci 2022; 24:ijms24010412. [PMID: 36613855 PMCID: PMC9820537 DOI: 10.3390/ijms24010412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
In this study, we identified a new citrus vein enation virus (CVEV) isolate (named CVEV-DT1) through sRNA high-throughput sequencing and traditional sequencing. Phylogenetic analysis based on whole genome sequences of all known CVEV isolates revealed that CVEV-DT1 was in an evolutionary branch with other isolates from China. Molecular variation analysis showed that the single nucleotide variability along CVEV full-length sequences was less than 8%, with more transitions (60.55%) than transversions (39.43%), indicating a genetically homogeneous CVEV population. In addition, non-synonymous nucleotide mutations mainly occurred in ORF1 and ORF2. Based on disorder analysis of all encoded ORF by CVEV-DT1, we identified that the CVEV-DT1 coat protein (CP) formed spherical granules, mainly in the cell nucleus and partly throughout the cytoplasm, with liquid properties through subcellular localization and photobleaching assay. Furthermore, we also confirmed that the CVEV P0 protein has weak post-transcriptional RNA-silencing suppressor activity and could elicit a strong hypersensitive response (HR) in tobacco plants. Collectively, to the best of our knowledge, our study was the first to profile the genomic variation in all the reported CVEV isolates and reveal the functions of CVEV-DT1-encoded proteins.
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Affiliation(s)
- Runqiu Dou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qingqing Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fengzhe Yu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongxia Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yajuan Qian
- State Key Laboratory of Rice Biology, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-571-88982677
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Li X, Hu W, Li Y, Li Y, Chen S, Wang J. Development of an RT-LAMP assay for the detection of maize yellow mosaic virus in maize. J Virol Methods 2021; 300:114384. [PMID: 34856307 DOI: 10.1016/j.jviromet.2021.114384] [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: 09/01/2020] [Revised: 10/12/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Maize is one of the most widely cultivated cereal crops worldwide. Maize yellow mosaic virus (MaYMV) (species Maize yellow mosaic virus, genus Polerovirus and family Luteoviridae) was first reported in maize from China. In this study, a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting MaYMV. The optimal concentrations of betaine, Mg2+ and dNTPs for the assay were 0 M, 1.4 mM and 6 mM, respectively, and the optimal reaction time was 50 min. Using total plant RNA as the template, the detection limit of the RT-LAMP assay for MaYMV was 1 pg, while that of RT-PCR was 100 pg, indicating that the RT-LAMP assay developed was 100 times more sensitive than RT-PCR. Importantly, the RT-LAMP assay successfully detected MaYMV using rapidly extracted crude RNA from infected maize as a template. In conclusion, the RT-LAMP assay developed was a rapid, specific, sensitive and low-cost method for the detection of MaYMV in field samples of maize.
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Affiliation(s)
- Xiaoqin Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Wenli Hu
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Yu Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Yan Li
- Yunnan Plant Protection and Quarantine Station, Kunming, 650034, China
| | - Suiyun Chen
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Jianguang Wang
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China.
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Saleem A, Ali Z, Yeh SD, Saeed W, Binat Imdad A, Akbar MF, Goodman RE, Naseem S. Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya. PLoS One 2021; 16:e0258298. [PMID: 34637470 PMCID: PMC8509892 DOI: 10.1371/journal.pone.0258298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 09/23/2021] [Indexed: 11/23/2022] Open
Abstract
Papaya ringspot virus biotype-P is a detrimental pathogen of economically important papaya and cucurbits worldwide. The mutation prone feature of this virus perhaps accounts for its geographical dissemination. In this study, investigations of the atypical PRSV-P strain was conducted based on phylogenetic, recombination and genetic differentiation analyses considering of it's likely spread across India and Bangladesh. Full length genomic sequences of 38 PRSV isolates and 35 CP gene sequences were subjected to recombination analysis. A total of 61 recombination events were detected in aligned complete PRSV genome sequences. 3 events were detected in complete genome of PRSV strain PK whereas one was in its CP gene sequence. The PRSV-PK appeared to be recombinant of a major parent from Bangladesh. However, the genetic differentiation based on full length genomic sequences revealed less frequent gene flow between virus PRSV-PK and the population from America, India, Colombia, other Asian Countries and Australia. Whereas, frequent gene flow exists between Pakistan and Bangladesh virus populations. These results provided evidence correlating geographical position and genetic distances. We speculate that the genetic variations and evolutionary dynamics of this virus may challenge the resistance developed in papaya against PRSV and give rise to virus lineage because of its atypical emergence where geographic spread is already occurring.
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Affiliation(s)
- Anam Saleem
- Department of Biosciences, Plant Biotechnology and Molecular Pharming Lab, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Zahid Ali
- Department of Biosciences, Plant Biotechnology and Molecular Pharming Lab, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Shyi-Dong Yeh
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Wajeeha Saeed
- Department of Biosciences, Plant Biotechnology and Molecular Pharming Lab, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Amna Binat Imdad
- Department of Biosciences, Plant Biotechnology and Molecular Pharming Lab, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Muhammad Faheem Akbar
- Department of Agriculture and Agribusiness Management, University of Karachi, Karachi, Pakistan
| | - Richard E. Goodman
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Saadia Naseem
- Department of Biosciences, Plant Biotechnology and Molecular Pharming Lab, COMSATS University Islamabad (CUI), Islamabad, Pakistan
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First report of Maize yellow mosaic virus (MaYMV) infecting sugarcane in India and its molecular characterization. AUSTRALASIAN PLANT PATHOLOGY 2021. [DOI: 10.1007/s13313-021-00809-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Comparative genomics reveals insights into genetic variability and molecular evolution among sugarcane yellow leaf virus populations. Sci Rep 2021; 11:7149. [PMID: 33785787 PMCID: PMC8009895 DOI: 10.1038/s41598-021-86472-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/15/2021] [Indexed: 11/08/2022] Open
Abstract
Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775-5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1-G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0-24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.
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