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Renukadevi P, Devi RG, Jothika C, Karthikeyan G, Malathi VG, Balakrishnan N, Rajagopal B, Nakkeeran S, Abd-Allah EF. Genomic distinctiveness and recombination in tomato leaf curl New Delhi virus (ToLCNDV-BG) isolates infecting bitter gourd. 3 Biotech 2024; 14:184. [PMID: 39070236 PMCID: PMC11282025 DOI: 10.1007/s13205-024-04009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/14/2024] [Indexed: 07/30/2024] Open
Abstract
There are two begomoviruses, tomato leaf curl New Delhi virus (ToLCNDV) and bitter gourd yellow mosaic virus (BgYMV) infecting bitter gourd in India. An extensive survey conducted from 2019 to 2022 clearly established that infection by ToLCNDV is more predominant (92.43%) than BgYMV (44%). The ToLCNDV isolates infecting bitter gourd shared only 88% identity in the DNA-A component with other ToLCNDV isolates and were found to be a distinct variant. The predicted amino acid sequence of the viral proteins, replication initiation protein, coat protein, and the symptom determinant protein in the study isolates are markedly different. Especially the RCR motif I and RCR motif III are different from other geminiviruses. Infectivity of cloned components of one of the isolates ToLCNDV-BG NP was demonstrated in bitter gourd. Recombination analysis clearly revealed that the study isolates are recombinants with the major parent predicted as squash leaf curl Yunnan virus (GenBank Accession Number: MK064241) and the minor parent as ToLCNDV from Pakistan (GenBank Accession Number: AM747291). Due to distinct genomic features and less than 90% identity with the majority of ToLCNDV isolates, the study isolates deserve to be raised to the status of a distinct strain, designated as ToLCNDV-BG. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04009-3.
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Affiliation(s)
- P. Renukadevi
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003 India
| | - R. Gomathi Devi
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003 India
| | - C. Jothika
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003 India
| | - G. Karthikeyan
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003 India
| | - V. G. Malathi
- GI, Sree Kumaran Hill Crest Apartment, Coimbatore, Tamil Nadu 641046 India
| | - N. Balakrishnan
- Directorate of Research, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003 India
| | - B. Rajagopal
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003 India
| | - S. Nakkeeran
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003 India
| | - Elsayed Fathi Abd-Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, 11451 Riyadh, Saudi Arabia
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Lagzian A, Ghorbani A, Tabein S, Riseh RS. Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis. BMC Genomics 2024; 25:736. [PMID: 39080552 PMCID: PMC11289972 DOI: 10.1186/s12864-024-10649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.
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Affiliation(s)
- Arezoo Lagzian
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute, Karaj, Iran.
| | - Saeid Tabein
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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Wang D, Yin Y, Zhang X, Ye J. An Interspecies Recombinant Sida Yellow Mosaic China Virus Isolate and Betasatellite Cause a Leaf Curl Disease in Tobacco in Hainan, China. PLANT DISEASE 2024; 108:877-886. [PMID: 37743589 DOI: 10.1094/pdis-07-23-1346-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: 09/26/2023]
Abstract
Tobacco (Nicotiana tabacum) is an herbaceous crop. Cigar tobacco, a group of tobacco cultivars, has recently been planted in a few provinces in China. Since its introduction, symptoms such as leaf curling and vein thickening have appeared. Here we report a begomovirus, Sida yellow mosaic China virus-Hainan isolate (designated SiYMCNV-HN), associated with the betasatellite (designated SiYMCNB-HN) as the causal agent of a leaf curl disease in cigar tobacco (N. tabacum cv. Haiyan101) in Hainan Province, China. Phylogenetic and recombination analyses indicate that SiYMCNV-HN is an interspecies recombinant with a SiYMCNV isolate as the major parent and a Sida yellow vein Vietnam virus isolate as the minor parent. Full-length infectious clones of SiYMCNV-HN and SiYMCNB-HN were generated, which were highly infectious and induced high pathogenicity through agroinfiltration in Nicotiana benthamiana and N. tabacum. This newly reported recombinant begomovirus poses potential threats to tobacco plantations in the region.
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Affiliation(s)
- Duan Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuteng Yin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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Puthanveed V, Singh K, Poimenopoulou E, Pettersson J, Siddique AB, Kvarnheden A. Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus. PHYTOPATHOLOGY 2023; 113:1788-1798. [PMID: 36802872 DOI: 10.1094/phyto-11-22-0446-v] [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: 06/18/2023]
Abstract
Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA, and TuYV was detected in all fields except one. In the counties of Skåne, Kalmar, and Östergötland, the average incidence of TuYV-infected plants was 75%, and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed coinfection with TuYV-associated RNA. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV, together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Vinitha Puthanveed
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Khushwant Singh
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague 161 06, Czech Republic
| | - Efstratia Poimenopoulou
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Josefin Pettersson
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Abu Bakar Siddique
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anders Kvarnheden
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Fan Y, Zhong Y, Pan L, Wang X, Ding M, Liu S. A shift of vector specificity acquired by a begomovirus through natural homologous recombination. MOLECULAR PLANT PATHOLOGY 2023; 24:882-895. [PMID: 37191666 PMCID: PMC10346445 DOI: 10.1111/mpp.13351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023]
Abstract
Recombination is common in plant viruses such as geminiviruses, but the ecological and pathogenic consequences have been explored only in a few cases. Here, we found that a new begomovirus, tomato yellow leaf curl Shuangbai virus (TYLCSbV), probably originated from the recombination of Ageratum yellow vein China virus (AYVCNV) and tobacco curl shoot virus (TbCSV). Agrobacterium-mediated inoculation showed that TYLCSbV and AYVCNV have similar levels of infectivity on tomato and tobacco plants. However, the two viruses exhibit contrasting specificities for vector transmission, that is, TYLCSbV was efficiently transmitted by the whitefly Bemisia tabaci Mediterranean (MED) rather than by the whitefly B. tabaci Middle East-Asia Minor 1 (MEAM1), whereas AYVCNV was more efficiently transmitted by MEAM1. We also showed that the transmission efficiencies of TYLCSbV and AYVCNV are positively correlated with the accumulation of the viruses in whitefly whole bodies and organs/tissues. The key coat protein amino acids that determine their accumulation are between positions 147 and 256. Moreover, field surveys suggest that MED has displaced MEAM1 in some regions where TYLCSbV was collected. Viral competition assays indicated that TYLCSbV outcompeted AYVCNV when transmitted by MED, while the outcome was the opposite when transmitted by MEAM1. Our findings suggest that recombination has resulted in a shift of vector specificity that could provide TYLCSbV with a potential selective transmission advantage, and the population shift of whitefly cryptic species could have influenced virus evolution towards an extended trajectory of transmission.
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Affiliation(s)
- Yun‐Yun Fan
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yu‐Wei Zhong
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Li‐Long Pan
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Xiao‐Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Ming Ding
- Biotechnology and Germplasm Resources InstituteYunnan Academy of Agricultural SciencesKunmingChina
| | - Shu‐Sheng Liu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
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Fortes IM, Fernández-Muñoz R, Moriones E. Crinivirus Tomato Chlorosis Virus Compromises the Control of Tomato Yellow Leaf Curl Virus in Tomato Plants by the Ty-1 Gene. PHYTOPATHOLOGY 2023; 113:1347-1359. [PMID: 36690608 DOI: 10.1094/phyto-09-22-0334-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Tomato yellow leaf curl disease (TYLCD) causes severe damage to tomato crops in warm regions of the world, and is associated with infections of several whitefly (Bemisia tabaci)-transmitted single-stranded (ss)DNA begomoviruses (genus Begomovirus, family Geminiviridae). The most widespread begomovirus isolates associated with TYLCD are those of the type strain of the Tomato yellow leaf curl virus species, known as Israel (TYLCV-IL). The Ty-1 gene is widely used in commercial tomato cultivars to control TYLCV-IL damage, providing resistance to the virus by restricting viral accumulation and tolerance to TYLCD by inhibiting disease symptoms. However, several reports suggest that TYLCV-IL-like isolates are adapting to the Ty-1 gene and are causes of concern for possibly overcoming the provided control. This is the case with TYLCV-IL IS76-like recombinants that have a small genome fragment acquired by genetic exchange from an isolate of Tomato yellow leaf curl Sardinia virus, another begomovirus species associated with TYLCD. Here we show that TYLCV-IL IS76-like isolates partially break down the TYLCD-tolerance provided by the Ty-1 gene and that virulence differences might exist between isolates. Interestingly, we demonstrate that mixed infections with an isolate of the crinivirus (genus Crinivirus, family Closteroviridae) species Tomato chlorosis virus (ToCV), an ssRNA virus also transmitted by B. tabaci and emerging worldwide in tomato crops, boosts the breakdown of the TYLCD-tolerance provided by the Ty-1 gene either with TYLCV-IL IS76-like or canonical TYLCV-IL isolates. Moreover, we demonstrate the incorporation of the Ty-2 gene in Ty-1-commercial tomatoes to restrict (no virus or virus traces, no symptoms) systemic infections of recombinant TYLCV-IL IS76-like and canonical TYLCV-IL isolates, even in the presence of ToCV infections, which provides more robust and durable control of TYLCD.
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Affiliation(s)
- Isabel M Fortes
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Rafael Fernández-Muñoz
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM), Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
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Fiallo-Olivé E, Navas-Castillo J. Begomoviruses: what is the secret(s) of their success? TRENDS IN PLANT SCIENCE 2023; 28:715-727. [PMID: 36805143 DOI: 10.1016/j.tplants.2023.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 05/13/2023]
Abstract
Begomoviruses constitute an extremely successful group of emerging plant viruses transmitted by whiteflies of the Bemisia tabaci complex. Hosts include important vegetable, root, and fiber crops grown in the tropics and subtropics. Factors contributing to the ever-increasing diversity and success of begomoviruses include their predisposition to recombine their genomes, interaction with DNA satellites recruited throughout their evolution, presence of wild plants as a virus reservoir and a source of speciation, and extreme polyphagia and continuous movement of the insect vectors to temperate regions. These features as well as some controversial issues (replication in the insect vector, putative seed transmission, transmission by insects other than B. tabaci, and expansion of the host range to monocotyledonous plants) will be analyzed in this review.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
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Nigam D, Muthukrishnan E, Flores-López LF, Nigam M, Wamaitha MJ. Comparative Genome Analysis of Old World and New World TYLCV Reveals a Biasness toward Highly Variable Amino Acids in Coat Protein. PLANTS (BASEL, SWITZERLAND) 2023; 12:1995. [PMID: 37653912 PMCID: PMC10223811 DOI: 10.3390/plants12101995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 09/02/2023]
Abstract
Begomoviruses, belonging to the family Geminiviridae and the genus Begomovirus, are DNA viruses that are transmitted by whitefly Bemisia tabaci (Gennadius) in a circulative persistent manner. They can easily adapt to new hosts and environments due to their wide host range and global distribution. However, the factors responsible for their adaptability and coevolutionary forces are yet to be explored. Among BGVs, TYLCV exhibits the broadest range of hosts. In this study, we have identified variable and coevolving amino acid sites in the proteins of Tomato yellow leaf curl virus (TYLCV) isolates from Old World (African, Indian, Japanese, and Oceania) and New World (Central and Southern America). We focused on mutations in the coat protein (CP), as it is highly variable and interacts with both vectors and host plants. Our observations indicate that some mutations were accumulating in Old World TYLCV isolates due to positive selection, with the S149N mutation being of particular interest. This mutation is associated with TYLCV isolates that have spread in Europe and Asia and is dominant in 78% of TYLCV isolates. On the other hand, the S149T mutation is restricted to isolates from Saudi Arabia. We further explored the implications of these amino acid changes through structural modeling. The results presented in this study suggest that certain hypervariable regions in the genome of TYLCV are conserved and may be important for adapting to different host environments. These regions could contribute to the mutational robustness of the virus, allowing it to persist in different host populations.
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Affiliation(s)
- Deepti Nigam
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University (TTU), Lubbock, TX 79409, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | | | - Luis Fernando Flores-López
- Departamento de Biotecnología y Bioquímica, Centro de Investigacióny de Estudios Avanzados de IPN (CINVESTAV) Unidad Irapuato, Irapuato 368224, Mexico
| | - Manisha Nigam
- Department of Biochemistry, Hemvati Nandan Bahuguna Garhwal University, Srinagar 246174, Uttarakhand, India
| | - Mwathi Jane Wamaitha
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi P.O. Box 14733-00800, Kenya
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Noris E, Pegoraro M, Palzhoff S, Urrejola C, Wochner N, Kober S, Ruoff K, Matić S, Schnepf V, Weisshaar N, Wege C. Differential Effects of RNA-Dependent RNA Polymerase 6 (RDR6) Silencing on New and Old World Begomoviruses in Nicotiana benthamiana. Viruses 2023; 15:v15040919. [PMID: 37112899 PMCID: PMC10143181 DOI: 10.3390/v15040919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
RNA-dependent RNA polymerases (RDRs) are key players in the antiviral defence mediated by RNA silencing in plants. RDR6 is one of the major components of the process, regulating the infection of certain RNA viruses. To better clarify its function against DNA viruses, we analyzed the effect of RDR6 inactivation (RDR6i) in N. benthamiana plants on two phloem-limited begomoviruses, the bipartite Abutilon mosaic virus (AbMV) and the monopartite tomato yellow leaf curl Sardinia virus (TYLCSV). We observed exacerbated symptoms and DNA accumulation for the New World virus AbMV in RDR6i plants, varying with the plant growth temperature (ranging from 16 °C to 33 °C). However, for the TYLCSV of Old World origin, RDR6 depletion only affected symptom expression at elevated temperatures and to a minor extent; it did not affect the viral titre. The accumulation of viral siRNA differed between the two begomoviruses, being increased in RDR6i plants infected by AbMV but decreased in those infected by TYLCSV compared to wild-type plants. In situ hybridization revealed a 6.5-fold increase in the number of AbMV-infected nuclei in RDR6i plants but without egress from the phloem tissues. These results support the concept that begomoviruses adopt different strategies to counteract plant defences and that TYLCSV evades the functions exerted by RDR6 in this host.
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Affiliation(s)
- Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy
| | - Mattia Pegoraro
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy
| | - Sandra Palzhoff
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Catalina Urrejola
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Nicolai Wochner
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Sigi Kober
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Kerstin Ruoff
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy
| | - Vera Schnepf
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Nina Weisshaar
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Christina Wege
- Institute of Biomaterials and Biomolecular Systems, Molecular and Synthetic Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
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Fiallo-Olivé E, Navas-Castillo J. The Role of Extensive Recombination in the Evolution of Geminiviruses. Curr Top Microbiol Immunol 2023; 439:139-166. [PMID: 36592245 DOI: 10.1007/978-3-031-15640-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mutation, recombination and pseudo-recombination are the major forces driving the evolution of viruses by the generation of variants upon which natural selection, genetic drift and gene flow can act to shape the genetic structure of viral populations. Recombination between related virus genomes co-infecting the same cell usually occurs via template swapping during the replication process and produces a chimeric genome. The family Geminiviridae shows the highest evolutionary success among plant virus families, and the common presence of recombination signatures in their genomes reveals a key role in their evolution. This review describes the general characteristics of members of the family Geminiviridae and associated DNA satellites, as well as the extensive occurrence of recombination at all taxonomic levels, from strain to family. The review also presents an overview of the recombination patterns observed in nature that provide some clues regarding the mechanisms involved in the generation and emergence of recombinant genomes. Moreover, the results of experimental evolution studies that support some of the conclusions obtained in descriptive or in silico works are summarized. Finally, the review uses a number of case studies to illustrate those recombination events with evolutionary and pathological implications as well as recombination events in which DNA satellites are involved.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain.
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11
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Jammes M, Urbino C, Diouf MB, Peterschmitt M. Refining the emergence scenario of the invasive recombinant Tomato yellow leaf curl virus -IS76. Virology 2023; 578:71-80. [PMID: 36473279 DOI: 10.1016/j.virol.2022.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
TYLCV-IS76, a unique recombinant between tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), has replaced its parental viruses in southern Morocco. To refine its emergence scenario, its fitness was monitored experimentally in conditions aiming at reproducing natural situations, i.e. superinfection of plants already infected with parental viruses and competition with other TYLCV/TYLCSV recombinants (LSRec) automatically generated in plants coinfected with TYLCV and TYLCSV. TYLCV-IS76 accumulated significantly more than parental viruses regardless of plant age and superinfection delay. Although TYLCV-IS76 and LSRec both accumulated more than parental viruses in laboratory conditions, LSRec were displaced by TYLCV-IS76 in nature like parental viruses were. TYLCV-IS76 did not exhibit any vector transmission advantage over LSRec and TYLCV the most competitive parental virus. Thus, it is apparently only in the plant compartment that the recombination event that generated TYLCV-IS76, induced the competitiveness advantage by which the last became first.
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Affiliation(s)
- Margaux Jammes
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Cica Urbino
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mame Boucar Diouf
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Michel Peterschmitt
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
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12
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Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics. Viruses 2022; 14:v14112481. [PMID: 36366579 PMCID: PMC9693158 DOI: 10.3390/v14112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.
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13
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Lal A, Kil EJ, Vo TTB, Wira Sanjaya IGNP, Qureshi MA, Nattanong B, Ali M, Shuja MN, Lee S. Interspecies Recombination-Led Speciation of a Novel Geminivirus in Pakistan. Viruses 2022; 14:v14102166. [PMID: 36298721 PMCID: PMC9612148 DOI: 10.3390/v14102166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/25/2022] Open
Abstract
Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed spread worldwide. Here, we present the molecular characterization of a novel recombinant begomovirus identified from C. album in Lahore, Pakistan. The complete DNA- A genome of the virus associated with the leaf distortion occurred in the infected C. album plants was cloned and sequenced. DNA sequence analysis showed that the nucleotide sequence of the virus shared 93% identity with those of the rose leaf curl virus and the duranta leaf curl virus. Interestingly, this newly identified virus is composed of open reading frames (ORFs) from different origins. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the sequences. The infectious clone of the newly detected virus was found to be fully infectious in C. album and Nicotiana benthamiana as the viral DNA was successfully reconstituted from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. Our study reveals a new speciation of an emergent ssDNA plant virus associated with C. album through recombination and therefore, proposed the tentative name 'Chenopodium leaf distortion virus' (CLDV).
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong 36729, Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong 36729, Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong 36729, Korea
| | - Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
| | | | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
| | - Muhammad Ali
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore 54770, Pakistan
| | - Malik Nawaz Shuja
- Department of Microbiology, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea
- Correspondence:
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14
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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
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15
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Lai X, Wang H, Wu C, Zheng W, Leng J, Zhang Y, Yan L. Comparison of Potato Viromes Between Introduced and Indigenous Varieties. Front Microbiol 2022; 13:809780. [PMID: 35602024 PMCID: PMC9114672 DOI: 10.3389/fmicb.2022.809780] [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: 11/05/2021] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Viral disease in potatoes has been a major problem in potato production worldwide. In addition to the potential risk of introducing new diseases in new areas, viral-disease epidemics/pandemics can be initiated by “spillover” of indigenous viruses from infected alternative hosts into introduced cultivars. To investigate the tendency of potential viral infection/resistance, we analyzed the viromes of introduced and indigenous varieties of potatoes among different tissues using RNA-seq libraries. Bioinformatics analyses revealed that potato viruses PVM, PVY, and PVS were dominant and the most frequently identified viruses infecting potato virus-free plants in the field, and showed an infection bias between introduced and indigenous cultivars. PVY and PVS were the major viruses in introduced varieties, whereas PVM showed an extraordinarily high percentage in the indigenous variety. Other three common viruses, PVH, potato mop-top virus, and potato leafroll virus were identified specifically in the indigenous variety. There was a tendency for tissue-specific infection and sequence variation in viruses: underground parts (tubers, roots) harbored more unusual viruses, and tubers harbored relatively more variation with a high frequency of single nucleotide polymorphisms than other tissues. Taken together, our study provides a comprehensive overview of the composition, distribution, and sequence variation of viruses between introduced and indigenous varieties of potatoes.
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Affiliation(s)
- Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Haiyan Wang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Caiyun Wu
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Wen Zheng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Jing Leng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Yizheng Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
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16
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Complete genome sequence of a novel bipartite begomovirus infecting the legume weed Macroptilium erythroloma. Arch Virol 2022; 167:1597-1602. [PMID: 35562613 DOI: 10.1007/s00705-022-05410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 01/27/2022] [Indexed: 11/02/2022]
Abstract
The natural occurrence of mixed infections and large populations of the polyphagous vector (Bemisia tabaci) are the main factors associated with the intensification of the genetic flow among begomoviruses in Neotropical areas, contributing to the emergence of novel recombinants. Here, high-throughput sequencing and metagenomic analyses were employed to discover and characterize a novel recombinant bipartite begomovirus, tentatively named "macroptilium bright yellow interveinal virus" (MaBYIV) in the weed Macroptilium erythroloma (Fabaceae). Recombination signals were detected in MaBYIV, involving bean golden mosaic virus (BGMV) and tomato mottle leaf curl virus (ToMoLCV) genome components. All of the original MaBYIV-infected M. erythroloma plants were found to have mixed infections with BGMV. MaBYIV was transmitted to bean and soybean cultivars via B. tabaci MEAM 1, indicating that M. erythroloma may play a role as a year-round reservoir of a potential new viral pathogen of economically important legume crops.
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17
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Moradi Z. Meta-transcriptomic analysis reveals an isolate of aphid lethal paralysis virus from Wisteria sinensis in Iran. Virus Res 2022; 315:198770. [DOI: 10.1016/j.virusres.2022.198770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/21/2022]
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18
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Bashir S, Naqvi SMS, Muhammad A, Hussain I, Ali K, Khan MR, Farrakh S, Yasmin T, Hyder MZ. Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes. PLoS One 2022; 17:e0263875. [PMID: 35255085 PMCID: PMC8901069 DOI: 10.1371/journal.pone.0263875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/30/2022] [Indexed: 11/30/2022] Open
Abstract
Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.
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Affiliation(s)
- Sana Bashir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aish Muhammad
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Iqbal Hussain
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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19
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Mendes ALSF, Melo AM, Ramos-Sobrinho R, Silva SJC, Ferro CG, Ferro MMM, Murilo Zerbini F, Lima GSA, Assunção IP. High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens. Arch Virol 2021; 166:3289-3299. [PMID: 34554304 DOI: 10.1007/s00705-021-05245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/07/2021] [Indexed: 11/26/2022]
Abstract
Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright's F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.
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Affiliation(s)
- Adso L S F Mendes
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Aline M Melo
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | | | - Sarah J C Silva
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Camila G Ferro
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo, Piracicaba, 13418-900, Brazil
| | - Mayra M M Ferro
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Gaus S A Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Iraildes P Assunção
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil.
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20
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Xavier CAD, Godinho MT, Mar TB, Ferro CG, Sande OFL, Silva JC, Ramos-Sobrinho R, Nascimento RN, Assunção I, Lima GSA, Lima ATM, Murilo Zerbini F. Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis. Mol Ecol 2021; 30:3747-3767. [PMID: 34021651 DOI: 10.1111/mec.15997] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 12/17/2022]
Abstract
Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of divided (bipartite) genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. Here, we performed a parallel evolutionary analysis of the DNA-A and DNA-B segments of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analysed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both segments, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate segments belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and segments.
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Affiliation(s)
- César A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Talita B Mar
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Osvaldo F L Sande
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - José C Silva
- Dep. de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Roberto Ramos-Sobrinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Renato N Nascimento
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Iraildes Assunção
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Gaus S A Lima
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Alison T M Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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21
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Farooq T, Umar M, She X, Tang Y, He Z. Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites. Virus Evol 2021; 7:veab054. [PMID: 34532058 PMCID: PMC8438885 DOI: 10.1093/ve/veab054] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity, and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China, while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite's virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite, and Cotton leaf curl Multan betasatellite populations arising from distinct regions exhibit high mutation rates. Although evolutionarily linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.
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Affiliation(s)
- Tahir Farooq
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Muhammad Umar
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia
| | - Xiaoman She
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Yafei Tang
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Zifu He
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
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22
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Bertin S, Parrella G, Nannini M, Guercio G, Troiano E, Tomassoli L. Distribution and Genetic Variability of Bemisia tabaci Cryptic Species (Hemiptera: Aleyrodidae) in Italy. INSECTS 2021; 12:insects12060521. [PMID: 34199806 PMCID: PMC8229085 DOI: 10.3390/insects12060521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 11/16/2022]
Abstract
Bemisia tabaci is a key pest of horticultural, fibre and ornamental crops worldwide, primarily as a vector of plant viruses. In Italy, B. tabaci has established since the 1980s-1990s in southern regions as well as in Sicily and Sardinia. Recent reports of infestations in some areas of central Italy prompted a new survey to assess the whitefly distribution in the country as well as to update the species and haplotype composition of the populations present in southern Italy and in the main islands. The survey confirmed that B. tabaci is nowadays established in central Italy even at more northern latitudes than those noticed before. Most of the specimens collected throughout the country belonged to the Mediterranean (MED) species. The MEDQ1 and Q2 haplogroups were prevailing in open-field and greenhouse cultivations, respectively, except in Sardinia where only Q1 specimens were found on a wide range of crops and weeds. Population genetics analyses showed that several MEDQ1 haplotypes currently occur in Italy and their distribution is unrelated to evident temporal and geographic trends, except for a new genetic variant which seems to have originated in Sardinia. The MED species is known to better adapt to insecticide treatments and high temperatures, and its northward spread in Italy may have been favoured by the intensive agricultural practices and steady increase in both winter and summer temperatures occurring in the last few decades. The extensive presence of B. tabaci in Italy proves that a strict surveillance for possible new outbreaks of whitefly-transmitted viruses should be addressed to a range of sites that are expanding northwards.
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Affiliation(s)
- Sabrina Bertin
- CREA Research Centre for Plant Protection and Certification, via C.G. Bertero 22, 00156 Rome, Italy; (G.G.); (L.T.)
- Correspondence: ; Tel.: +39-06-8207-0242
| | - Giuseppe Parrella
- National Research Council, Institute for Sustainable Plant Protection (CNR-IPSP), Piazzale Enrico Fermi 1, Napoli, 80055 Portici, Italy; (G.P.); (E.T.)
| | - Mauro Nannini
- Agris Sardegna, Servizio Ricerca Studi Ambientali, Difesa delle Colture e Qualità Delle Produzioni, Viale Trieste 111, 09123 Cagliari, Italy;
| | - Giorgia Guercio
- CREA Research Centre for Plant Protection and Certification, via C.G. Bertero 22, 00156 Rome, Italy; (G.G.); (L.T.)
| | - Elisa Troiano
- National Research Council, Institute for Sustainable Plant Protection (CNR-IPSP), Piazzale Enrico Fermi 1, Napoli, 80055 Portici, Italy; (G.P.); (E.T.)
| | - Laura Tomassoli
- CREA Research Centre for Plant Protection and Certification, via C.G. Bertero 22, 00156 Rome, Italy; (G.G.); (L.T.)
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23
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Sacristán S, Goss EM, Eves-van den Akker S. How Do Pathogens Evolve Novel Virulence Activities? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:576-586. [PMID: 33522842 DOI: 10.1094/mpmi-09-20-0258-ia] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, U.S.A
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Disease Pandemics and Major Epidemics Arising from New Encounters between Indigenous Viruses and Introduced Crops. Viruses 2020; 12:v12121388. [PMID: 33291635 PMCID: PMC7761969 DOI: 10.3390/v12121388] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/13/2023] Open
Abstract
Virus disease pandemics and epidemics that occur in the world’s staple food crops pose a major threat to global food security, especially in developing countries with tropical or subtropical climates. Moreover, this threat is escalating rapidly due to increasing difficulties in controlling virus diseases as climate change accelerates and the need to feed the burgeoning global population escalates. One of the main causes of these pandemics and epidemics is the introduction to a new continent of food crops domesticated elsewhere, and their subsequent invasion by damaging virus diseases they never encountered before. This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops. This spillover requires new encounters at the managed and natural vegetation interface. The principal virus disease pandemic examples described are two (cassava mosaic, cassava brown streak) that threaten food security in sub-Saharan Africa (SSA), and one (tomato yellow leaf curl) doing so globally. A further example describes a virus disease pandemic threatening a major plantation crop producing a vital food export for West Africa (cacao swollen shoot). Also described are two examples of major virus disease epidemics that threaten SSA’s food security (rice yellow mottle, groundnut rosette). In addition, brief accounts are provided of two major maize virus disease epidemics (maize streak in SSA, maize rough dwarf in Mediterranean and Middle Eastern regions), a major rice disease epidemic (rice hoja blanca in the Americas), and damaging tomato tospovirus and begomovirus disease epidemics of tomato that impair food security in different world regions. For each pandemic or major epidemic, the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution, are explained. Finally, clarification is provided over what needs to be done globally to achieve effective management of severe virus disease pandemics and epidemics initiated by spillover events.
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25
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Koeda S, Fujiwara I, Oka Y, Kesumawati E, Zakaria S, Kanzaki S. Ty-2 and Ty-3a Conferred Resistance are Insufficient Against Tomato Yellow Leaf Curl Kanchanaburi Virus from Southeast Asia in Single or Mixed Infections of Tomato. PLANT DISEASE 2020; 104:3221-3229. [PMID: 33044916 DOI: 10.1094/pdis-03-20-0613-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV), a monopartite begomovirus that originated in the eastern Mediterranean, has spread worldwide, becoming a serious threat to tomato (Solanum lycopersicum L.) production. Southeast Asia is considered one of the hotspots for begomovirus diversity, and a wide variety of local begomovirus species distinct from TYLCV have been identified. In this study, the protection effect of introgressions of single TYLCV Ty resistance genes, Ty-2 and Ty-3a, in tomato was examined against inoculations of the bipartite begomoviruses Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) and Pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated from Indonesia. Our findings suggest that Ty-2 in the heterozygous state was found to be ineffective against PepYLCIV and TYLCKaV, whereas Ty-3a in the heterozygous state was effective against PepYLCIV and partially effective against TYLCKaV. Quantification of viral DNAs showed correlation between symptom expression and viral DNA accumulation. Moreover, mixed infections of TYLCKaV and PepYLCIV caused notably severe symptoms in tomato plants harboring Ty-3a. In cases of mixed infection, quantifying viral DNAs showed a relatively high accumulation of PepYLCIV, indicating that Ty-3a loses its effectiveness against PepYLCIV when TYLCKaV is also present. This study demonstrates the lack of effectiveness of Ty resistance genes against single and mixed infections of distinct local begomoviruses from Southeast Asia.
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Affiliation(s)
- Sota Koeda
- Faculty of Agriculture, Kindai University, 3327-204 Nara, Japan
| | - Ikuya Fujiwara
- Graduate School of Agriculture, Kindai University, 3327-204 Nara, Japan
| | - Yuki Oka
- Faculty of Agriculture, Kindai University, 3327-204 Nara, Japan
| | - Elly Kesumawati
- Faculty of Agriculture, Syiah Kuala University, 23111 Banda Aceh, Aceh, Indonesia
| | - Sabaruddin Zakaria
- Faculty of Agriculture, Syiah Kuala University, 23111 Banda Aceh, Aceh, Indonesia
| | - Shinya Kanzaki
- Faculty of Agriculture, Kindai University, 3327-204 Nara, Japan
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26
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Nefedeva M, Titov I, Tsybanov S, Malogolovkin A. Recombination shapes African swine fever virus serotype-specific locus evolution. Sci Rep 2020; 10:18474. [PMID: 33116230 PMCID: PMC7794389 DOI: 10.1038/s41598-020-75377-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/05/2020] [Indexed: 11/08/2022] Open
Abstract
The recombination is one of the most frequently identified drivers of double-stranded DNA viruses evolution. However, the recombination events in African swine fever virus (ASFV) genomes have been poorly annotated. We hypothesize that the genetic determinants of ASFV variability are potential hot-spots for recombination. Here, we analyzed ASFV serotype-specific locus (C-type lectin (EP153R) and CD2v (EP402R)) in order to allocate the recombination breakpoints in these immunologically important proteins and reveal driving forces of virus evolution. The recombinations were found in both proteins, mostly among ASFV strains from East Africa, where multiple virus transmission cycles are notified. The recombination events were essentially associated with the domain organization of proteins. The phylogenetic analysis demonstrated the lack of clonal evolution for African strains which conclusively support the significance of recombinations in the serotype-specific locus. In addition, the signature of adaptive evolution of these two genes, pN/pS > 1, was demonstrated. These results have implications for the interpretation of cross-protection potential between evolutionary distant ASFV strains and strongly suggest that C-type lectin and CD2v may experience substantial selective pressure than previously thought.
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Affiliation(s)
- Mariia Nefedeva
- Federal Research Center for Virology and Microbiology, Volginsky, Russia
| | - Ilya Titov
- Federal Research Center for Virology and Microbiology, Volginsky, Russia
| | - Sodnom Tsybanov
- Federal Research Center for Virology and Microbiology, Volginsky, Russia
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Prasad A, Sharma N, Hari-Gowthem G, Muthamilarasan M, Prasad M. Tomato Yellow Leaf Curl Virus: Impact, Challenges, and Management. TRENDS IN PLANT SCIENCE 2020; 25:897-911. [PMID: 32371058 DOI: 10.1016/j.tplants.2020.03.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 05/26/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most studied plant viral pathogens because it is the most damaging virus for global tomato production. In order to combat this global threat, it is important that we understand the biology of TYLCV and devise management approaches. The prime objective of this review is to highlight management strategies for efficiently tackling TYLCV epidemics and global spread. For that purpose, we focus on the impact TYLCV has on worldwide agriculture and the role of recent advances for our understanding of TYLCV interaction with its host and vector. Another important focus is the role of recombination and mutations in shaping the evolution of TYLCV genome and geographical distribution.
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Affiliation(s)
- Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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28
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Mahmoudieh M, Noor MRM, Harikrishna JA, Othman RY. Identification and characterization of Ageratum yellow vein Malaysia virus (AYVMV) and an associated betasatellite among begomoviruses infecting Solanum lycopersicum in Malaysia. J Appl Genet 2020; 61:619-628. [PMID: 32808206 DOI: 10.1007/s13353-020-00574-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/06/2020] [Accepted: 08/11/2020] [Indexed: 11/27/2022]
Abstract
The study describes results of a survey of tomato fields for the presence of begomoviruses from different regions of Peninsular Malaysia. An ORF-based (C2 and C3) study was performed to determine the distribution of begomoviruses associated with a severe leaf curl disease in tomato-growing areas of Peninsular Malaysia. Viral DNA was isolated from symptomatic tomato plants, and begomovirus association was confirmed by PCR using DNA-A degenerate primers. The C2 and C3 sequences of the putative begomoviruses were similar to two corresponded ORFs of different geographically separated strains of begomoviruses: Pepper yellow leaf curl Indonesia virus and Tomato yellow leaf curl Kanchanaburi virus. The present study also identified a unique isolate, Ageratum yellow vein Malaysia virus (AYVMV) among above mentioned survey. It has a single-stranded DNA component and its associated betasatellite. The single-stranded DNA component is consisting of 2750 nt with six open reading frames and an organization resembling that of monopartite geminiviruses. The full length of viral single-stranded DNA component genome obtained using next generation sequencing (NGS) showed the highest sequence identity (99%) with Ageratum yellow vein virus (AYVV-BA). The betasatellite component genome obtained by NGS has 1342 nt and showed the highest sequence identity (91%) with the Pepper yellow leaf curl betasatellite. Following ICTV guidelines, Ageratum yellow vein Malaysia virus was assigned the abbreviation AYVMV with sequence and phylogenetic analysis indicating that it might have evolved by recombination of two or more viral ancestors.
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Affiliation(s)
- Mohtaram Mahmoudieh
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Mohamad Roff Mohd Noor
- Horticulture Research Centre, MARDI Headquarters, P.O.Box 12301, GPO, 50774, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rofina Yasmin Othman
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
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Li Z, Du Z, Tang Y, She X, Wang X, Zhu Y, Yu L, Lan G, He Z. C4, the Pathogenic Determinant of Tomato Leaf Curl Guangdong Virus, May Suppress Post-transcriptional Gene Silencing by Interacting With BAM1 Protein. Front Microbiol 2020; 11:851. [PMID: 32431688 PMCID: PMC7215500 DOI: 10.3389/fmicb.2020.00851] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/09/2020] [Indexed: 12/27/2022] Open
Abstract
Tomato leaf curl Guangdong virus (ToLCGdV) is a begomovirus associated with a Tomato yellow leaf curl disease (TYLCD) epidemic in Guangdong province, China. Being the least conserved protein among geminivirus proteins, the function of C4 during ToLCGdV infection has not been elucidated. In this study, the infectious clones of ToLCGdV and a ToLCGdV mutant (ToLCGdVmC4) with disrupted C4 ORF were constructed. Although ToLCGdV and ToLCGdVmC4 could infect Nicotiana benthamiana and tomato plants, ToLCGdVmC4 elicited much milder symptoms compared with ToLCGdV. To further verify the role of C4 in viral pathogenesis, C4 was expressed in N. benthamiana from Potato virus X (PVX) vector. The results showed that ToLCGdV C4 enhanced the pathogenicity of PVX and induced more severe developmental abnormalities in plants compared with PVX alone or PVX-mC4. In addition, ToLCGdV C4 suppresses systemic gene silencing in the transgenic N. benthamiana line 16c, but not local gene silencing induced by sense GFP in wild-type N. benthamiana plants. Moreover, C4 suppresses transcriptional gene silencing (TGS) by reducing the DNA methylation level of 35S promoter in 16c-TGS N. benthamiana plants. Furthermore, C4 could also interact with the receptor-like kinase (RLK) BARELY ANY MERISTEM 1 (BAM1), suggesting that C4 may suppress gene silencing by interfering with the function of BAM1 in the cell-to-cell spread of RNAi. All these results suggest that C4 is a pathogenic determinant of ToLCGdV, and C4 may suppress post-transcriptional gene silencing (PTGS) by interacting with BAM1.
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Affiliation(s)
- Zhenggang Li
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zhenguo Du
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yafei Tang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoman She
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaomei Wang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanhua Zhu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lin Yu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guobing Lan
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zifu He
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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30
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Marchant WG, Gautam S, Hutton SF, Srinivasan R. Tomato Yellow Leaf Curl Virus-Resistant and -Susceptible Tomato Genotypes Similarly Impact the Virus Population Genetics. FRONTIERS IN PLANT SCIENCE 2020; 11:599697. [PMID: 33365041 PMCID: PMC7750400 DOI: 10.3389/fpls.2020.599697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/13/2020] [Indexed: 05/14/2023]
Abstract
Tomato yellow leaf curl virus is a species in the genus Begomovirus and family Geminiviridae. Tomato yellow leaf curl virus (TYLCV) infection induces severe symptoms on tomato plants and causes serious yield losses worldwide. TYLCV is persistently transmitted by the sweetpotato whitefly, Bemisia tabaci (Gennadius). Cultivars and hybrids with a single or few genes conferring resistance against TYLCV are often planted to mitigate TYLCV-induced losses. These resistant genotypes (cultivars or hybrids) are not immune to TYLCV. They typically develop systemic infection, display mild symptoms, and produce more marketable tomatoes than susceptible genotypes under TYLCV pressure. In several pathosystems, extensive use of resistant cultivars with single dominant resistance-conferring gene has led to intense selection pressure on the virus, development of highly virulent strains, and resistance breakdown. This study assessed differences in TYLCV genomes isolated from susceptible and resistant genotypes in Florida and Georgia. Phylogenetic analyses indicated that Florida and Georgia isolates were distinct from each other. Population genetics analyses with genomes field-collected from resistant and susceptible genotypes from Florida and/or Georgia provided no evidence of a genetic structure between the resistant and susceptible genotypes. No codons in TYLCV genomes from TYLCV-resistant or susceptible genotypes were under positive selection, suggesting that highly virulent or resistance-breaking TYLCV strains might not be common in tomato farmscapes in Florida and Georgia. With TYLCV-resistant genotypes usage increasing recently and multiple tomato crops being planted during a calendar year, host resistance-induced selection pressure on the virus remains a critical issue. To address the same, a greenhouse selection experiment with one TYLCV-resistant and susceptible genotype was conducted. Each genotype was challenged with TYLCV through whitefly-mediated transmission serially 10 times (T1-T10). Population genetics parameters at the genome level were assessed at T1, T5, and T10. Results indicated that genomes from resistant and susceptible genotypes did not differentiate with increasing transmission number, no specific mutations were repeatedly observed, and no positive selection was detected. These results reiterate that resistance in tomato might not be exerting selection pressure against TYLCV to facilitate development of resistance-breaking strains. TYLCV populations rather seem to be shaped by purifying selection and/or population expansion.
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Affiliation(s)
- Wendy G. Marchant
- Department of Entomology, University of Georgia, Tifton, GA, United States
| | - Saurabh Gautam
- Department of Entomology, University of Georgia, Griffin, GA, United States
| | - Samuel F. Hutton
- Horticulture Sciences Department, University of Florida, Wimauma, FL, United States
| | - Rajagopalbabu Srinivasan
- Department of Entomology, University of Georgia, Griffin, GA, United States
- *Correspondence: Rajagopalbabu Srinivasan
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31
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Pérez-Padilla V, Fortes IM, Romero-Rodríguez B, Arroyo-Mateos M, Castillo AG, Moyano C, De León L, Moriones E. Revisiting Seed Transmission of the Type Strain of Tomato yellow leaf curl virus in Tomato Plants. PHYTOPATHOLOGY 2020; 110:121-129. [PMID: 31584339 DOI: 10.1094/phyto-07-19-0232-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Isolates of the Tomato yellow leaf curl virus (TYLCV) species (genus Begomovirus, family Geminiviridae) infect tomato crops worldwide, causing severe economic damage. Members of the whitefly Bemisia tabaci sibling species group are the vector of begomoviruses, including TYLCV. However, transmission of isolates of the type strain (Israel [IL]) of TYLCV (TYLCV-IL) by tomato seed has recently been reported based on infections occurring in Korea. Because of the consequences of this finding on the epidemiology and control of the disease caused by TYLCV and on the seed market, it was considered essential to revisit and expand those results to other tomato-growing areas. TYLCV DNA content was detected in tomato and Nicotiana benthamiana seed collected from plants naturally or experimentally infected with TYLCV-IL, supporting its seedborne nature. The TYLCV-IL replication detected in tomato and N. benthamiana flower reproductive organs demonstrated close association of this virus with the seed during maturation. However, the significant reduction of TYLCV DNA load after surface disinfections of tomato seed suggests that most of the virus is located externally, as contaminant of the seed coat. Transmission assays, carried out with seven tomato genotypes and more than 3,000 tomato plants, revealed no evidence of seed transmission from "surface-disinfected" or untreated seed for two Mediterranean isolates of TYLCV-IL. Similar results were also obtained for seed collected from TYLCV-IL-infected N. benthamiana plants. The results support the conclusion that TYLCV-IL is seedborne but is not seed transmitted in tomato or N. benthamiana, suggesting that transmission through seed is not a general property of TYLCV.
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Affiliation(s)
- Verónica Pérez-Padilla
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de La Coruña, km 7.5, E-28040 Madrid, Spain
| | - Isabel M Fortes
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
| | - Beatriz Romero-Rodríguez
- IHSM-UMA-CSIC, Área de Genética, Facultad de Ciencias, Universidad de Málaga, E-29071, Málaga, Spain
| | - Manuel Arroyo-Mateos
- IHSM-UMA-CSIC, Área de Genética, Facultad de Ciencias, Universidad de Málaga, E-29071, Málaga, Spain
| | - Araceli G Castillo
- IHSM-UMA-CSIC, Área de Genética, Facultad de Ciencias, Universidad de Málaga, E-29071, Málaga, Spain
| | - Cristina Moyano
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de La Coruña, km 7.5, E-28040 Madrid, Spain
| | - Leandro De León
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. de La Coruña, km 7.5, E-28040 Madrid, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental "La Mayora", E-29750 Algarrobo-Costa, Málaga, Spain
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32
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Rodríguez-Negrete EA, Morales-Aguilar JJ, Domínguez-Duran G, Torres-Devora G, Camacho-Beltrán E, Leyva-López NE, Voloudakis AE, Bejarano ER, Méndez-Lozano J. High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico. Viruses 2019; 11:v11070594. [PMID: 31261973 PMCID: PMC6669537 DOI: 10.3390/v11070594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022] Open
Abstract
Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.
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Affiliation(s)
- Edgar Antonio Rodríguez-Negrete
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Juan José Morales-Aguilar
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gustavo Domínguez-Duran
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gadiela Torres-Devora
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Erika Camacho-Beltrán
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Norma Elena Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Andreas E Voloudakis
- Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, 75 Iera Odos, Athens 11855, Greece
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico.
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33
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García-Arenal F, Zerbini FM. Life on the Edge: Geminiviruses at the Interface Between Crops and Wild Plant Hosts. Annu Rev Virol 2019; 6:411-433. [PMID: 31180812 DOI: 10.1146/annurev-virology-092818-015536] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. Studies on the epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses' potential to emerge in crops.
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Affiliation(s)
- Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain;
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), and National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
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Idris AM, Al-Saleh MA, M Zakri A, Brown JK. Minimal genomic variability in Merremia mosaic virus isolates endemic in Merremia spp and cultivated tomato in Puerto Rico. Virusdisease 2019; 30:84-94. [PMID: 31143835 PMCID: PMC6517463 DOI: 10.1007/s13337-017-0412-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 11/15/2017] [Indexed: 11/24/2022] Open
Abstract
Merremia mosaic virus (MerMV), a bipartite begomovirus, was identified for the first time as a pathogen of commercial tomato plantings. Infection of tomato by MerMV caused mild leaf curling and yellow foliar mosaic symptoms. Herein, the MerMV was identified in symptomatic Merremia quinquefolia and M. aegyptia (Convolvulaceae) plants exhibiting bright yellow or yellow-green foliar mosaic symptoms, respectively. The full-length begomoviral components were amplified from total DNA isolated from two wild species of Merremia and commercial tomato plants during 1991-1998. The DNA was subjected to rolling circle amplification, restriction digestion, and DNA sequencing. The resultant 19 and 26 apparently full-length DNA-A and DNA-B components were ~ 2557 and ~ 2492 bases, respectively. The 140-base common region was 97.9% identical between DNA-A and -B components, a predictive evidence for cognate DNA-A and -B components. Although the DNA-A components were highly conserved at 96-100%, the DNA-B components diverged at ~ 89 to 100%, respectively. The overall clonal genomic features strongly suggested that MerMV lineage has been under host-selection for some time, and only recently, has undergone a host-shift, putatively, from wild convolvulaceous species to tomato (Solanaceae). Phylogenetically, MerMV grouped with other bipartite begomoviruses indigenous to the Caribbean region, with MerMV DNA-A components forming three clusters, and the DNA-B components grouped in one clade. Both clades contained only one closet relative, an isolate of MerMV from Venezuela, MerMV-VE. Biolistic inoculation of M. quinquefolia and tomato seedlings with the DNA-A and -B components of PR68 and PR80 resulted in development of symptoms like those observed in naturally-infected species, respectively.
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Affiliation(s)
- Ali M. Idris
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
| | - M. A. Al-Saleh
- Plant Protection Department, King Saud University, Riyadh, Saudi Arabia
| | - A. M Zakri
- Plant Protection Department, King Saud University, Riyadh, Saudi Arabia
| | - J. K. Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
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Fiallo-Olivé E, Trenado HP, Louro D, Navas-Castillo J. Recurrent speciation of a tomato yellow leaf curl geminivirus in Portugal by recombination. Sci Rep 2019; 9:1332. [PMID: 30718735 PMCID: PMC6362282 DOI: 10.1038/s41598-018-37971-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/18/2018] [Indexed: 11/09/2022] Open
Abstract
Recurrent evolution can involve interspecific interactions, recognized to play a primary role in the diversification and organization of life. Both in the plant and animal kingdoms, the recurrent formation of allopolyploid species has been described. In the virosphere, recombination between isolates of different species has been shown to be a source of speciation. In this work, complete genome analysis showed that speciation through recombination of an emergent DNA plant virus, tomato yellow leaf curl Malaga virus (genus Begomovirus, family Geminiviridae), has occurred independently in Portugal and Spain, confirming previous observations with tomato yellow leaf curl Axarquia virus, also originated independently in Spain and Italy. These results will guide future research to discover new cases of recurrent emergence of recombinant virus species in geographical areas where the putative parents co-exist or can be introduced. This will reveal the role that recurrent speciation through recombination plays in the evolution of the virosphere and will help to understand the consequences of this phenomenon on the diversification of life.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas - Universidad de Málaga (IHSM-CSIC-UMA), Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain
| | - Helena P Trenado
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas - Universidad de Málaga (IHSM-CSIC-UMA), Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain
| | - Diamantina Louro
- Instituto Nacional dos Recursos Biológicos (INRB), Quinta do Marquês, Oeiras, Portugal
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas - Universidad de Málaga (IHSM-CSIC-UMA), Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain.
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Díaz-Pendón JA, Sánchez-Campos S, Fortes IM, Moriones E. Tomato Yellow Leaf Curl Sardinia Virus, a Begomovirus Species Evolving by Mutation and Recombination: A Challenge for Virus Control. Viruses 2019; 11:E45. [PMID: 30634476 PMCID: PMC6356960 DOI: 10.3390/v11010045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/28/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022] Open
Abstract
The tomato leaf curl disease (TYLCD) is associated with infections of several species of begomoviruses (genus Begomovirus, family Geminiviridae) and causes severe damage to tomatoes throughout tropical and sub-tropical regions of the world. Among others, the Tomato yellow leaf curl Sardinia virus (TYLCSV) species causes damage in the Mediterranean Basin since early outbreaks occurred. Nevertheless, scarce information is available about the diversity of TYLCSV. Here, we study this aspect based on the sequence information accessible in databases. Isolates of two taxonomically differentiated TYLCSV strains can be found in natural epidemics. Their evolution is mostly associated with mutation combined with selection and random genetic drift and also with inter-species recombination which is frequent in begomoviruses. Moreover, a novel putative inter-strain recombinant is reported. Although no significantly new biological behaviour was observed for this latter recombinant, its occurrence supports that as shown for other related begomoviruses, recombination continues to play a central role in the evolution of TYLCD-associated viruses and the dynamism of their populations. The confrontation of resistant tomatoes with isolates of different TYLCD-associated viruses including the novel recombinant demonstrates the existence of a variable virus x plant genotype interaction. This has already been observed for other TYLCD-associated viruses and is a challenge for the control of their impact on tomato production.
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Affiliation(s)
- Juan A Díaz-Pendón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| | - Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| | - Isabel María Fortes
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
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Torre C, Donaire L, Gómez-Aix C, Juárez M, Peterschmitt M, Urbino C, Hernando Y, Agüero J, Aranda MA. Characterization of Begomoviruses Sampled during Severe Epidemics in Tomato Cultivars Carrying the Ty-1 Gene. Int J Mol Sci 2018; 19:E2614. [PMID: 30177671 PMCID: PMC6164481 DOI: 10.3390/ijms19092614] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/27/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae) is a major species that causes a tomato disease for which resistant tomato hybrids (mainly carriers of the Ty-1/Ty-3 gene) are being used widely. We have characterized begomoviruses severely affecting resistant tomato crops in Southeast Spain. Circular DNA was prepared from samples by rolling circle amplification, and sequenced by massive sequencing (2015) or cloning and Sanger sequencing (2016). Thus, 23 complete sequences were determined, all belonging to the TYLCV Israel strain (TYLCV-IL). Massive sequencing also revealed the absence of other geminiviral and beta-satellite sequences. A phylogenetic analysis showed that the Spanish isolates belonged to two groups, one related to early TYLCV-IL isolates in the area (Group 1), and another (Group 2) closely related to El Jadida (Morocco) isolates, suggesting a recent introduction. The most parsimonious evolutionary scenario suggested that the TYLCV isolates of Group 2 are back recombinant isolates derived from TYLCV-IS76, a recombinant virus currently predominating in Moroccan epidemics. Thus, an infectious Group 2 clone (TYLCV-Mu15) was constructed and used in in planta competition assays against TYLCV-IS76. TYLCV-Mu15 predominated in single infections, whereas TYLCV-IS76 did so in mixed infections, providing credibility to a scenario of co-occurrence of both types of isolates.
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Affiliation(s)
- Covadonga Torre
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Livia Donaire
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
| | - Cristina Gómez-Aix
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel Juárez
- Escuela Politécnica Superior de Orihuela, Universidad Miguel Hernández de Elche, Ctra. de Beniel, Km 3.2, 03312 Alicante, Spain.
| | - Michel Peterschmitt
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Cica Urbino
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD), UMR-BGPI, Equipe Interactions Virus-Insecte-Plante, TA A-54/K, Campus International de Baillarguet, CEDEX 5, 34398 Monptellier, France.
| | - Yolanda Hernando
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Jesús Agüero
- Abiopep S.L., Departamento de I + D + i, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2°, 30100 Murcia, Spain.
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, P.O. Box 164, 30100 Murcia, Spain.
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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Sánchez-Campos S, Domínguez-Huerta G, Díaz-Martínez L, Tomás DM, Navas-Castillo J, Moriones E, Grande-Pérez A. Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences. FRONTIERS IN PLANT SCIENCE 2018; 9:932. [PMID: 30013589 PMCID: PMC6036239 DOI: 10.3389/fpls.2018.00932] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/11/2018] [Indexed: 05/12/2023]
Abstract
Geminiviruses (family Geminiviridae) possess single-stranded circular DNA genomes that are replicated by cellular polymerases in plant host cell nuclei. In their hosts, geminivirus populations behave as ensembles of mutant and recombinant genomes, known as viral quasispecies. This favors the emergence of new geminiviruses with altered host range, facilitating new or more severe diseases or overcoming resistance traits. In warm and temperate areas several whitefly-transmitted geminiviruses of the genus Begomovirus cause the tomato yellow leaf curl disease (TYLCD) with significant economic consequences. TYLCD is frequently controlled in commercial tomatoes by using the dominant Ty-1 resistance gene. Over a 45 day period we have studied the diversification of three begomoviruses causing TYLCD: tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl Malaga virus (TYLCMaV, a natural recombinant between TYLCV and TYLCSV). Viral quasispecies resulting from inoculation of geminivirus infectious clones were examined in plants of susceptible tomato (ty-1/ty-1), heterozygous resistant tomato (Ty-1/ty-1), common bean, and the wild reservoir Solanum nigrum. Differences in virus fitness across hosts were observed while viral consensus sequences remained invariant. However, the complexity and heterogeneity of the quasispecies were high, especially in common bean and the wild host. Interestingly, the presence or absence of the Ty-1 allele in tomato did not lead to differences in begomovirus mutant spectra. However, the fitness decrease of TYLCSV and TYLCV in tomato at 45 dpi might be related to an increase in CP (Coat protein) mutation frequency. In Solanum nigrum the recombinant TYLCMaV, which showed lower fitness than TYLCSV, at 45 dpi actively explored Rep (Replication associated protein) ORF but not the overlapping C4. Our results underline the importance of begomovirus mutant spectra during infections. This is especially relevant in the wild reservoir of the viruses, which has the potential to maintain highly diverse mutant spectra without modifying their consensus sequences.
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Affiliation(s)
- Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Guillermo Domínguez-Huerta
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| | - Luis Díaz-Martínez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| | - Diego M. Tomás
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
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Simón A, Ruiz L, Velasco L, Janssen D. Absolute Quantification of Tomato leaf curl New Delhi virus Spain strain, ToLCNDV-ES: Virus Accumulation in a Host-Specific Manner. PLANT DISEASE 2018; 102:165-171. [PMID: 30673467 DOI: 10.1094/pdis-06-17-0840-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) (family Geminiviridae, genus Begomovirus) has recently been introduced in western Mediterranean countries. Isolates in Spain constitute a new strain, denominated ToLCNDV-ES, that is causing losses in commercial zucchini and melon crops; however, it is also, although less often, detected in commercial tomato crops. We developed a tissue-print hybridization test to detect the two genomic components of the virus and a TaqMan quantitative polymerase chain reaction (qPCR) test to estimate the number of genome copies in plants. qPCR was approximately 104 to 106 times more sensitive than tissue-print hybridization to detect viral genomic DNA-A and DNA-B, respectively. It also detected the virus in more experimentally and naturally ToLCNDV-ES-infected zucchini squash and tomato plants. ToLCNDV-ES DNA-A titers were significantly lower in tomato than in zucchini plants, often falling below the detection limits in the hybridization test. In addition, the DNA-B accumulation was impaired in tomato when compared with zucchini. According to the data obtained in this study, the differences in viral titers of both plant species contribute to explain the dissimilarities in symptom expression, capability of detection, and transmission of the virus.
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Affiliation(s)
- Almudena Simón
- IFAPA Centro La Mojonera, La Mojonera 04745, Almería, Spain
| | - Leticia Ruiz
- IFAPA Centro La Mojonera, La Mojonera 04745, Almería, Spain
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Belabess Z, Urbino C, Granier M, Tahiri A, Blenzar A, Peterschmitt M. The typical RB76 recombination breakpoint of the invasive recombinant tomato yellow leaf curl virus of Morocco can be generated experimentally but is not positively selected in tomato. Virus Res 2017; 243:44-51. [PMID: 28988981 DOI: 10.1016/j.virusres.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
Abstract
TYLCV-IS76 is an unusual recombinant between the highly recombinogenic tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), two Mediterranean begomoviruses (Geminiviridae). In contrast with the previously reported TYLCV/TYLCSV recombinants, it has a TYLCSV derived fragment of only 76 nucleotides, and has replaced its parental viruses in natural conditions (Morocco, Souss region). The viral population shift coincided with the deployment of the popular Ty-1 resistant tomato cultivars, and according to experimental studies, has been driven by a strong positive selection in such resistant plants. However, although Ty-1 cultivars were extensively used in Mediterranean countries, TYLCV-IS76 was not reported outside Morocco. This, in combination with its unusual recombination pattern suggests that it was generated through a rare and possibly multistep process. The potential generation of a recombination breakpoint (RB) at locus 76 (RB76) was investigated over time in 10 Ty-1 resistant and 10 nearly isogenic susceptible tomato plants co-inoculated with TYLCV and TYLCSV clones. RB76 could not be detected in the recombinant progeny using the standard PCR/sequencing approach that was previously designed to monitor the emergence of TYLCV-IS76 in Morocco. Using a more sensitive PCR test, RB76 was detected in one resistant and five susceptible plants. The results are consistent with a very low intra-plant frequency of RB76 bearing recombinants throughout the test and support the hypothesis of a rare emergence of TYLCV-IS76. More generally, RBs were more scattered in resistant than in susceptible plants and an unusual RB at position 141 (RB141) was positively selected in the resistant cultivar; interestingly, RB141 bearing recombinants were detected in resistant tomato plants from the field. Scenarios of TYLCV-IS76 pre-emergence are proposed.
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Affiliation(s)
- Z Belabess
- CIRAD, UMR BGPI, 34398 Montpellier, France; Ecole Nationale d'Agriculture de Meknès, BPS 40 Meknès, Morocco; Faculté des Sciences de Meknès, BP 11201, Avenue Zitoune, Meknès, Morocco
| | - C Urbino
- CIRAD, UMR BGPI, 34398 Montpellier, France
| | - M Granier
- CIRAD, UMR BGPI, 34398 Montpellier, France
| | - A Tahiri
- Ecole Nationale d'Agriculture de Meknès, BPS 40 Meknès, Morocco
| | - A Blenzar
- Faculté des Sciences de Meknès, BP 11201, Avenue Zitoune, Meknès, Morocco
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Moriones E, Praveen S, Chakraborty S. Tomato Leaf Curl New Delhi Virus: An Emerging Virus Complex Threatening Vegetable and Fiber Crops. Viruses 2017; 9:E264. [PMID: 28934148 PMCID: PMC5691616 DOI: 10.3390/v9100264] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/13/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent. However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin. Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade. Special emphasis has been given to gene silencing suppression ability in order to counteract host plant defense responses. The importance of the interaction with DNA alphasatellites and betasatellites in the biology of the virus has been demonstrated. ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus. Recombination and pseudorecombination have been shown as motors of diversification and adaptive evolution. Important progress has also been made in control strategies to reduce disease damage. This review highlights these various achievements in the context of the previous knowledge of begomoviruses and their interactions with plants.
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Affiliation(s)
- Enrique Moriones
- Subtropical and Mediterranean Horticulture Institute "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La Mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Shelly Praveen
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110 012, India.
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.
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Chiquito-Almanza E, Acosta-Gallegos JA, García-Álvarez NC, Garrido-Ramírez ER, Montero-Tavera V, Guevara-Olvera L, Anaya-López JL. Simultaneous Detection of Both RNA and DNA Viruses Infecting Dry Bean and Occurrence of Mixed Infections by BGYMV, BCMV and BCMNV in the Central-West Region of Mexico. Viruses 2017; 9:E63. [PMID: 28358318 PMCID: PMC5408669 DOI: 10.3390/v9040063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 11/17/2022] Open
Abstract
A multiplex reverse transcription polymerase chain reaction (RT-PCR) assay was developed to simultaneously detect bean common mosaic virus (BCMV), bean common mosaic necrotic virus (BCMNV), and bean golden yellow mosaic virus (BGYMV) from common bean leaves dried with silica gel using a single total nucleic acid extraction cetyl trimethyl ammonium bromide (CTAB) method. A mixture of five specific primers was used to amplify three distinct fragments corresponding to 272 bp from the AC1 gene of BGYMV as well as 469 bp and 746 bp from the CP gene of BCMV and BCMNV, respectively. The three viruses were detected in a single plant or in a bulk of five plants. The multiplex RT-PCR was successfully applied to detect these three viruses from 187 field samples collected from 23 municipalities from the states of Guanajuato, Nayarit and Jalisco, Mexico. Rates of single infections were 14/187 (7.5%), 41/187 (21.9%), and 35/187 (18.7%), for BGYMV, BCMV, and BCMNV, respectively; 29/187 (15.5%) samples were co-infected with two of these viruses and 10/187 (5.3%) with the three viruses. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting these viruses in the common bean and can be used for routine molecular diagnosis and epidemiological studies.
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Affiliation(s)
- Elizabeth Chiquito-Almanza
- Instituto Tecnológico de Celaya, Departamento de Ingeniería Bioquímica, Celaya, Guanajuato, CP 38010, Mexico.
| | | | - Nadia C García-Álvarez
- INIFAP-Campo Experimental Santiago Ixcuintla, Santiago Ixcuintla, Nayarit, CP 63300, Mexico.
| | | | | | - Lorenzo Guevara-Olvera
- Instituto Tecnológico de Celaya, Departamento de Ingeniería Bioquímica, Celaya, Guanajuato, CP 38010, Mexico.
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44
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Lima ATM, Silva JCF, Silva FN, Castillo-Urquiza GP, Silva FF, Seah YM, Mizubuti ESG, Duffy S, Zerbini FM. The diversification of begomovirus populations is predominantly driven by mutational dynamics. Virus Evol 2017; 3:vex005. [PMID: 28458915 PMCID: PMC5399926 DOI: 10.1093/ve/vex005] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Begomoviruses (single-stranded DNA plant viruses) are responsible for serious agricultural threats. Begomovirus populations exhibit a high degree of within-host genetic variation and evolve as quickly as RNA viruses. Although the recombination-prone nature of begomoviruses has been extensively demonstrated, the relative contribution of recombination and mutation to the genetic variation of begomovirus populations has not been assessed. We estimated the genetic variability of begomovirus datasets from around the world. An uneven distribution of genetic variation across the length of the cp and rep genes due to recombination was evident from our analyses. To estimate the relative contributions of recombination and mutation to the genetic variability of begomoviruses, we mapped all substitutions over maximum likelihood trees and counted the number of substitutions on branches which were associated with recombination (ηr) and mutation (ημ). In addition, we also estimated the per generation relative rates of both evolutionary mechanisms (r/μ) to express how frequently begomovirus genomes are affected by recombination relative to mutation. We observed that the composition of genetic variation in all begomovirus datasets was dominated by mutation. Additionally, the low correlation between the estimates indicated that the relative contributions of recombination and mutation are not necessarily a function of their relative rates. Our results show that, although a considerable fraction of the genetic variation levels could be assigned to recombination, it was always lower than that due to mutation, indicating that the diversification of begomovirus populations is predominantly driven by mutational dynamics.
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Affiliation(s)
- Alison T M Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - José C F Silva
- National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Fábio N Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Gloria P Castillo-Urquiza
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Yee M Seah
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
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45
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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46
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Belabess Z, Peterschmitt M, Granier M, Tahiri A, Blenzar A, Urbino C. The non-canonical tomato yellow leaf curl virus recombinant that displaced its parental viruses in southern Morocco exhibits a high selective advantage in experimental conditions. J Gen Virol 2016; 97:3433-3445. [DOI: 10.1099/jgv.0.000633] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Zineb Belabess
- CIRAD-INRA-SupAgro, UMR BGPI, CIRAD, TA A -54K, Campus International de Baillarguet, F-34398 Montpellier, France
- Ecole Nationale d'Agriculture de Meknès, BPS 40, Meknès, Morocco
- Faculté des Sciences de Meknès BP 11201, Avenue Zitoune, Meknès, Morocco
| | - Michel Peterschmitt
- CIRAD-INRA-SupAgro, UMR BGPI, CIRAD, TA A -54K, Campus International de Baillarguet, F-34398 Montpellier, France
| | - Martine Granier
- CIRAD-INRA-SupAgro, UMR BGPI, CIRAD, TA A -54K, Campus International de Baillarguet, F-34398 Montpellier, France
| | | | - Abdelali Blenzar
- Faculté des Sciences de Meknès BP 11201, Avenue Zitoune, Meknès, Morocco
| | - Cica Urbino
- CIRAD-INRA-SupAgro, UMR BGPI, CIRAD, TA A -54K, Campus International de Baillarguet, F-34398 Montpellier, France
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47
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Fortes IM, Sánchez-Campos S, Fiallo-Olivé E, Díaz-Pendón JA, Navas-Castillo J, Moriones E. A Novel Strain of Tomato Leaf Curl New Delhi Virus Has Spread to the Mediterranean Basin. Viruses 2016; 8:E307. [PMID: 27834936 PMCID: PMC5127021 DOI: 10.3390/v8110307] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 10/31/2016] [Accepted: 11/07/2016] [Indexed: 11/16/2022] Open
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) is a whitefly-transmitted bipartite begomovirus (genus Begomovirus, family Geminiviridae) that causes damage to multiple cultivated plant species mainly belonging to the Solanaceae and Cucurbitaceae families. ToLCNDV was limited to Asian countries until 2012, when it was first reported in Spain, causing severe epidemics in cucurbit crops. Here, we show that a genetically-uniform ToLCNDV population is present in Spain, compatible with a recent introduction. Analyses of ToLCNDV isolates reported from other parts of the world indicated that this virus has a highly heterogeneous population genetically with no evident geographical, plant host or year-based phylogenetic groups observed. Isolates emerging in Spain belong to a strain that seems to have evolved by recombination. Isolates of this strain seem adapted to infecting cucurbits, but poorly infect tomatoes.
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Affiliation(s)
- Isabel M Fortes
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Sonia Sánchez-Campos
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Elvira Fiallo-Olivé
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Juan A Díaz-Pendón
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Jesús Navas-Castillo
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Enrique Moriones
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, La mayora Experimental Station, 29750 Algarrobo-Costa, Málaga, Spain.
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48
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Mabvakure B, Martin DP, Kraberger S, Cloete L, van Brunschot S, Geering ADW, Thomas JE, Bananej K, Lett JM, Lefeuvre P, Varsani A, Harkins GW. Ongoing geographical spread of Tomato yellow leaf curl virus. Virology 2016; 498:257-264. [PMID: 27619929 DOI: 10.1016/j.virol.2016.08.033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022]
Abstract
Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We undertook a temporally-scaled, phylogeographic analysis of all publicly available, full genome sequences of TYLCV, together with 70 new genome sequences from Australia, Iran and Mauritius. This revealed that whereas epidemics in Australia and China likely originated through multiple independent viral introductions from the East-Asian region around Japan and Korea, the New Caledonian epidemic was seeded by a variant from the Western Mediterranean region and the Mauritian epidemic by a variant from the neighbouring island of Reunion. Finally, we show that inter-continental scale movements of TYLCV to East Asia have, at least temporarily, ceased, whereas long-distance movements to the Americas and Australia are probably still ongoing.
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Affiliation(s)
- Batsirai Mabvakure
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Leendert Cloete
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
| | - Sharon van Brunschot
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Andrew D W Geering
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - John E Thomas
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Kaveh Bananej
- Department of Plant Virus Research, Iranian Research Institute of Plant Protection (IRIPP), Tehran 19395-1454, Iran
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l'IRAT, Saint-Pierre, Ile de la Réunion 97410, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l'IRAT, Saint-Pierre, Ile de la Réunion 97410, France
| | - 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, Private Bag 4800, Christchurch 8140, New Zealand; The Center for Functional Microbiomics, The Biodesign Institute and School of Life sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Gordon W Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
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49
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Sánchez-Campos S, Rodríguez-Negrete EA, Cruzado L, Grande-Pérez A, Bejarano ER, Navas-Castillo J, Moriones E. Tomato yellow leaf curl virus: No evidence for replication in the insect vector Bemisia tabaci. Sci Rep 2016; 6:30942. [PMID: 27476582 PMCID: PMC4967916 DOI: 10.1038/srep30942] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023] Open
Abstract
Begomovirus ssDNA plant virus (family Geminiviridae) replication within the Bemisia tabaci vector is controversial. Transovarial transmission, alteration to whitefly biology, or detection of viral transcripts in the vector are proposed as indirect evidence of replication of tomato yellow leaf curl virus (TYLCV). Recently, contrasting direct evidence has been reported regarding the capacity of TYLCV to replicate within individuals of B. tabaci based on quantitave PCR approaches. Time-course experiments to quantify complementary and virion sense viral nucleic acid accumulation within B. tabaci using a recently implemented two step qPCR procedure revealed that viral DNA quantities did not increase for time points up to 96 hours after acquisition of the virus. Our findings do not support a recent report claiming TYLCV replication in individuals of B. tabaci.
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Affiliation(s)
- Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Edgar A. Rodríguez-Negrete
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Lucía Cruzado
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Eduardo R. Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Área de Genética, Campus de Teatinos, 29071 Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
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50
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Monitoring the dynamics of emergence of a non-canonical recombinant of Tomato yellow leaf curl virus and displacement of its parental viruses in tomato. Virology 2015; 486:291-306. [DOI: 10.1016/j.virol.2015.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/13/2015] [Accepted: 09/22/2015] [Indexed: 11/23/2022]
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