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Liu Q, Wang Y, Zhang Z, Lv H, Qiao Q, Qin Y, Zhang D, Tian Y, Wang S, Li J. Diversity of Sweepoviruses Infecting Sweet Potato in China. PLANT DISEASE 2017; 101:2098-2103. [PMID: 30677378 DOI: 10.1094/pdis-04-17-0524-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sweepoviruses (a group of begomoviruses that infect plants in the family Convolvulaceae) have monopartite genomes that consist of a circular, single-stranded DNA molecule. Seventy-three complete genomic sequences of sweepoviruses were characterized from the sweet potato samples collected in China. Eight sweepovirus species, including two novel species with proposed names of Sweet potato leaf curl China virus 2 and Sweet potato leaf curl Sichuan virus 2, were identified among these samples. One species, Sweet potato leaf curl Canary virus, was first identified in China. Among the 13 identified strains of Chinese sweepoviruses, 4 were newly discovered. Sweet potato leaf curl virus had the highest frequency (53.4%) of occurrence in the sweet potato samples from China. The similarities among the 73 sweepovirus genomic sequences were between 77.6 and 100.0%. Multiple recombination events were identified, and 16 recombinant sequences were determined. Recombination was observed between different species and between different strains of the same species. Recombination breakpoints were mainly localized on the intergenic region and in three open reading frames (AC1, AV1, and AV2). This study is the first comprehensive report on the genetic diversity of sweepoviruses in China.
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Affiliation(s)
- Qili Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, P. R. China; College of Plant Protection, China Agricultural University, Beijing 100193; and College of Resources & Environmental Science, Henan Institute of Science and Technology, Xinxiang, P. R. China
| | - Yongjiang Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Zhenchen Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Hui Lv
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Qi Qiao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Yanhong Qin
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Desheng Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Yuting Tian
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Shuang Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences; and IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou 450002, P. R. China
| | - Jianqiang Li
- College of Plant Protection, China Agricultural University, Beijing
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Bi H, Fan W, Zhang P. C4 Protein of Sweet Potato Leaf Curl Virus Regulates Brassinosteroid Signaling Pathway through Interaction with AtBIN2 and Affects Male Fertility in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:1689. [PMID: 29021807 PMCID: PMC5623726 DOI: 10.3389/fpls.2017.01689] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/14/2017] [Indexed: 05/21/2023]
Abstract
Sweepoviruses have been identified globally and cause substantial yield losses and cultivar decline in sweet potato. This study aimed to investigate the interaction between sweepovirus and plant host by analyzing the function of the viral protein C4 of Sweet potato leaf curl virus-Jiangsu (SPLCV-JS), a sweepovirus cloned from diseased sweet potato plants in East China. Ectopic expression of the C4 in Arabidopsis altered plant development drastically with phenotypic changes including leaf curling, seedling twisting, deformation of floral tissues and reduction of pollen fertility, and seed number. Using bimolecular fluorescence complementation analysis, this study demonstrated that the SPLCV-JS C4 protein interacted with brassinosteroid-insensitive 2 (AtBIN2) in the plasma membrane of Nicotiana benthamiana cells. The C4 AtBIN2 interaction was further confirmed by yeast two-hybrid assays. This interaction led to the re-localization of AtBIN2-interacting proteins AtBES1/AtBZR1 into the nucleus which altered the expression of brassinosteroid (BR)-response genes, resulting in the activation of BR-signaling pathway. The interaction of SPLCV-JS C4 and AtBIN2 also led to the down-regulated expression of key genes involved in anther and pollen development, including SPROROCYTELESS/NOZZLE, DEFECTIVE IN TAPEL DEVELOPMENT AND FUNCTION 1, and ABORTED MICROSPORES, which caused abnormal tapetal development, followed by defective exine pattern formation of microspores and pollen release. Consequently, male fertility in the C4 transgenic Arabidopsis was reduced. The present study illustrated how the sweepovirus C4 protein functioned in host cells and affected male fertility by interacting with the key components of BR-signaling pathway.
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Affiliation(s)
- Huiping Bi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Weijuan Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Muhire BM, Varsani A, Martin DP. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 2014; 9:e108277. [PMID: 25259891 PMCID: PMC4178126 DOI: 10.1371/journal.pone.0108277] [Citation(s) in RCA: 860] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/26/2014] [Indexed: 01/16/2023] Open
Abstract
The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).
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Affiliation(s)
- Brejnev Muhizi Muhire
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Darren Patrick Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
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