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Positive selection and intrinsic disorder are associated with multifunctional C4(AC4) proteins and geminivirus diversification. Sci Rep 2021; 11:11150. [PMID: 34045539 PMCID: PMC8160170 DOI: 10.1038/s41598-021-90557-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses within the Geminiviridae family cause extensive agricultural losses. Members of four genera of geminiviruses contain a C4 gene (AC4 in geminiviruses with bipartite genomes). C4(AC4) genes are entirely overprinted on the C1(AC1) genes, which encode the replication-associated proteins. The C4(AC4) proteins exhibit diverse functions that may be important for geminivirus diversification. In this study, the influence of natural selection on the evolutionary diversity of 211 C4(AC4) genes relative to the C1(AC1) sequences they overlap was determined from isolates of the Begomovirus and Curtovirus genera. The ratio of nonsynonymous (dN) to synonymous (dS) nucleotide substitutions indicated that C4(AC4) genes are under positive selection, while the overlapped C1(AC1) sequences are under purifying selection. Ninety-one of 200 Begomovirus C4(AC4) genes encode elongated proteins with the extended regions being under neutral selection. C4(AC4) genes from begomoviruses isolated from tomato from native versus exotic regions were under similar levels of positive selection. Analysis of protein structure suggests that C4(AC4) proteins are entirely intrinsically disordered. Our data suggest that non-synonymous mutations and mutations that increase the length of C4(AC4) drive protein diversity that is intrinsically disordered, which could explain C4/AC4 functional variation and contribute to both geminivirus diversification and host jumping.
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Hosseinzadeh MR, Shams-Bakhsh M, Osaloo SK, Brown JK. Phylogenetic relationships, recombination analysis, and genetic variability among diverse variants of tomato yellow leaf curl virus in Iran and the Arabian Peninsula: further support for a TYLCV center of diversity. Arch Virol 2013; 159:485-97. [PMID: 24068582 DOI: 10.1007/s00705-013-1851-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022]
Abstract
The discovery of five strains of TYLCV in Iran, including the most well-known and widespread, TYLCV-IL, spurred a detailed study of the full-length genomes of additional TYLCV field isolates and an in-depth analysis of phylogenetic relationships, extent of recombination, and genetic variability of TYLCV isolates within Iran and throughout the Arabian Peninsula. Phylogenetic analysis of complete genome sequences of TYLCV isolates from Iran and other countries revealed four monophyletic clusters could be differentiated based on geographical origin, indicating that recent dispersal of these populations (by the vector or by humans) from these four regions has occurred minimally, or not at all. Genetic analysis revealed that TYLCV-IL isolates from southern Iran possessed greater genetic variability than the northeastern isolates, a pattern that may be reflective of evolution driven by geographically dependent isolation. Similarly, isolates of TYLCV-OM originating from Oman showed greater genetic variability than TYLCV-OM variants from Iran. Major recombination events, which were detected in all strains of TYLCV had breakpoints initiating in the C1, C1/C4, C2/C3 and V1 open reading frames (ORFs) and ending at the non-coding region and the C1, C1/C2 and C3 ORFs. Hence, these regions have consistently served as hot spots for recombination worldwide during the evolution of all currently recognized isolates and strains of TYLCV.
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Rocha CS, Castillo-Urquiza GP, Lima ATM, Silva FN, Xavier CAD, Hora-Júnior BT, Beserra-Júnior JEA, Malta AWO, Martin DP, Varsani A, Alfenas-Zerbini P, Mizubuti ESG, Zerbini FM. Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location. J Virol 2013; 87:5784-99. [PMID: 23487451 PMCID: PMC3648162 DOI: 10.1128/jvi.00155-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/04/2013] [Indexed: 01/21/2023] Open
Abstract
The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.
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Affiliation(s)
- Carolina S. Rocha
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gloria P. Castillo-Urquiza
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Alison T. M. Lima
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fábio N. Silva
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Cesar A. D. Xavier
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Braz T. Hora-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José E. A. Beserra-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Antonio W. O. Malta
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town, South Africa
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch, New Zealand
| | - Poliane Alfenas-Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Eduardo S. G. Mizubuti
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Sánchez-Campos S, Martínez-Ayala A, Márquez-Martín B, Aragón-Caballero L, Navas-Castillo J, Moriones E. Fulfilling Koch's postulates confirms the monopartite nature of tomato leaf deformation virus: a begomovirus native to the New World. Virus Res 2013; 173:286-93. [PMID: 23415858 DOI: 10.1016/j.virusres.2013.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/25/2013] [Accepted: 02/05/2013] [Indexed: 10/27/2022]
Abstract
The monopartite nature of the begomovirus tomato leaf deformation virus (ToLDeV) reported in Peru is demonstrated here. The DNA molecule cloned from an infected plant was shown to be fully infectious in tomatoes inducing leaf curling and stunted growth similar to that observed in field-infected plants. The viral DNA was reisolated from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. ToLDeV was demonstrated, therefore, as the causal agent of the disease syndrome widespread in tomato crops in Peru. This virus was shown to be present throughout the major tomato-growing regions of this country, both in tomatoes and wild plants. Analyses of the sequences of 51 ToLDeV isolates revealed a significant genetic diversity with three major genetic types co-circulating in the population. A geographical segregation was observed which should be taken into account for virus control. Constraints to genetic divergence found for the C4 gene of ToLDeV isolates suggest a relevant function for this protein. The results obtained confirm ToLDeV as a monopartite begomovirus native to the New World, which is a significant finding for this region.
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Affiliation(s)
- S Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental La Mayora, 29750 Algarrobo-Costa, Málaga, Spain
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da Silva SJC, Castillo-Urquiza GP, Hora Júnior BT, Assunção IP, Lima GSA, Pio-Ribeiro G, Mizubuti ESG, Zerbini FM. High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil. Arch Virol 2011; 156:2205-13. [PMID: 22006043 DOI: 10.1007/s00705-011-1119-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Accepted: 09/14/2011] [Indexed: 11/25/2022]
Abstract
Diseases caused by begomoviruses are a serious constraint to crop production in many tropical and subtropical areas of the world, including Brazil. Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants, which may act as natural reservoirs of viruses that cause epidemics in crop plants. Cleome affinis (family Capparaceae) is an annual weed that is frequently associated with leguminous crops in Brazil. Samples of C. affinis were collected in four states in the northeast of Brazil. Analysis of 14 full-length DNA-A components revealed that only one begomovirus was present, with 91-96% identity to cleome leaf crumple virus (ClLCrV). In a phylogenetic tree, ClLCrV forms a basal group relative to all other Brazilian begomoviruses. Evidence of multiple recombination events was detected among the ClLCrV isolates, which also display a high degree of genetic variability. Despite ClLCrV being the only begomovirus found, its phylogenetic placement, high genetic variability and recombinant nature suggest that C. affinis may act as a source of novel viruses for crop plants. Alternatively, ClLCrV could be a genetically isolated begomovirus. Further studies on the biological properties of ClLCrV should help to clarify the role of C. affinis in the epidemiological scenario of Brazilian begomoviruses.
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Affiliation(s)
- Sarah J C da Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, MG, Brazil
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Ooi K, Yahara T. Genetic variation of geminiviruses: comparison between sexual and asexual host plant populations. Mol Ecol 2008. [DOI: 10.1046/j.1365-294x.1999.00537.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- K. Ooi
- Department of Biology, Faculty of Science, Kyushu University, Hakozaki, Fukuoka 812‐8581, Japan
| | - T. Yahara
- Department of Biology, Faculty of Science, Kyushu University, Hakozaki, Fukuoka 812‐8581, Japan
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García-Andrés S, Accotto GP, Navas-Castillo J, Moriones E. Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the Mediterranean basin. Virology 2007; 359:302-12. [PMID: 17070885 DOI: 10.1016/j.virol.2006.09.030] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/10/2006] [Accepted: 09/19/2006] [Indexed: 11/28/2022]
Abstract
Tomato yellow leaf curl disease (TYLCD)-associated viruses present a highly structured population in the western Mediterranean basin, depending on host, geographical region and time. About 1,900 tomato and common bean samples were analyzed from which 111 isolates were characterized genetically based on a genome sequence that comprises coding and non-coding regions. Isolates of three distinct begomoviruses previously described were found (Tomato yellow leaf curl virus, TYLCV, Tomato yellow leaf curl Sardinia virus, TYLCSV, and Tomato yellow leaf curl Málaga virus, TYLCMalV), together with a novel recombinant virus. Mixed infections were detected in single plants, rationalizing the occurrence of recombinants. Except for TYLCV-type strain, single, undifferentiated subpopulations were present for each virus type, probably the result of founder effects. Limited genetic variation was observed in genomic regions, with selection against amino acid change in coding regions.
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Affiliation(s)
- Susana García-Andrés
- Estación Experimental "La Mayora", Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
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