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Ghorbani A, Faghihi MM, Falaki F, Izadpanah K. Complete genome sequencing and characterization of a potential new genotype of Citrus tristeza virus in Iran. PLoS One 2023; 18:e0288068. [PMID: 37384654 PMCID: PMC10310044 DOI: 10.1371/journal.pone.0288068] [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: 02/17/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023] Open
Abstract
Citrus tristeza virus (CTV) is one of the economically destructive viruses affecting citrus trees worldwide, causing significant losses in fruit production. Comparative genomic studies have shown genetic diversity in various regions of the genome of CTV isolates, which has classified the virus into several genotypes. In recent years, some orange citrumelo-tolerant rootstocks showed yellowing, decline, and vein clearing in northern Iran (Mazandaran province, Sari). We confirmed the presence of CTV in the symptomatic trees by reverse transcription PCR (RT-PCR). The complete genome of a Sari isolate of CTV (Sari isolate) was sequenced using next-generation sequencing (NGS) technology. In addition, phylogenetic analysis, differential gene expression of the virus and identification of its variants in a population were studied. We obtained the final contigs of the virus (nt) and annotated all genomes to viral ORFs, untranslated regions (UTRs), intergenic regions, and 5' and 3' ends of the genome. Phylogenetic analysis of the Sari isolate and other genotypes of CTV showed that the Sari isolates were placed in a distinct cluster without a sister group. Based on the number of specific transcripts (TPM) in CTV RNA -Seq, P13 was the most highly expressed gene related to the host range of the virus and its systemic infection. The ORFs of the polyprotein, P33, and P18 showed variation in a single population of the sari isolate. The CTV has a potential for variation in a population in a host, and these variations may contribute to the best fit of the CTV in different situations. In Iran, whole genome sequencing of the CTV was performed for the first time, and we gained new insights into CTV variation in a population.
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Affiliation(s)
- Abozar Ghorbani
- Nuclear Science and Technology Research Institute, Nuclear Agriculture Research School, Karaj, Iran
| | - Mohammad Mehdi Faghihi
- Plant Protection Research Department, Fars Agricultural and Natural Resources Research and Education Centre, AREEO, Zarghan, Iran
| | - Faezeh Falaki
- Department of Plant Protection, College of Agriculture Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Abstract
Viral interactions during multiple viral infections were examined in Agaricus bisporus cultures harboring 9 viruses (comprising 18 distinct viral RNAs) by statistically analyzing their relative abundance in fruitbodies. Four clusters of viral RNA were identified that suggested synergism and coreplication. Pairwise correlations revealed negative and positive correlations between clusters, indicating further synergisms and an antagonism involving a group containing a putative hypovirus and four nonhost ORFan RNAs (RNAs with no similarity to known sequences) possibly acting as defective interfering RNAs. The disease phenotype was observed in 10 to 15% of the fruitbodies apparently randomly located among asymptomatic fruitbodies. The degree of symptom expression consistently correlated with the levels of the multipartite virus AbV16. Diseased fruitbodies contained very high levels of AbV16 and AbV6 RNA2; these levels were orders of magnitude higher than those in asymptomatic tissues and were shown statistically to be discretely higher populations of abundance, indicating an exponential shift in the replicative capacity of the virus. High levels of AbV16 replication were specific to the fruitbody and not found in the underlying mycelium. There appeared to be a stochastic element occurring in these viral interactions, as observed in the distribution of diseased symptoms across a culture, differences in variance between experiments, and a number of additional viruses undergoing the step-jump in levels between experiments. Possible mechanisms for these multiple and simultaneous viral interactions in single culture are discussed in relation to known virus-host regulatory mechanisms for viral replication and whether additional factors could be considered to account for the 1,000-fold increase in AbV16 and AbV6 RNA2 levels.
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Chen AYS, Peng JHC, Polek M, Tian T, Ludman M, Fátyol K, Ng JCK. Comparative analysis identifies amino acids critical for citrus tristeza virus (T36CA) encoded proteins involved in suppression of RNA silencing and differential systemic infection in two plant species. MOLECULAR PLANT PATHOLOGY 2021; 22:64-76. [PMID: 33118689 PMCID: PMC7749750 DOI: 10.1111/mpp.13008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 05/06/2023]
Abstract
Complementary (c)DNA clones corresponding to the full-length genome of T36CA (a Californian isolate of Citrus tristeza virus with the T36 genotype), which shares 99.1% identity with that of T36FL (a T36 isolate from Florida), were made into a vector system to express the green fluorescent protein (GFP). Agroinfiltration of two prototype T36CA-based vectors (pT36CA) to Nicotiana benthamiana plants resulted in local but not systemic GFP expression/viral infection. This contrasted with agroinfiltration of the T36FL-based vector (pT36FL), which resulted in both local and systemic GFP expression/viral infection. A prototype T36CA systemically infected RNA silencing-defective N. benthamiana lines, demonstrating that a genetic basis for its defective systemic infection was RNA silencing. We evaluated the in planta bioactivity of chimeric pT36CA-pT36FL constructs and the results suggested that nucleotide variants in several open reading frames of the prototype T36CA could be responsible for its defective systemic infection. A single amino acid substitution in each of two silencing suppressors, p20 (S107G) and p25 (G36D), of prototype T36CA facilitated its systemic infectivity in N. benthamiana (albeit with reduced titre relative to that of T36FL) but not in Citrus macrophylla plants. Enhanced virus accumulation and, remarkably, robust systemic infection of T36CA in N. benthamiana and C. macrophylla plants, respectively, required two additional amino acid substitutions engineered in p65 (N118S and S158L), a putative closterovirus movement protein. The availability of pT36CA provides a unique opportunity for comparative analysis to identify viral coding and noncoding nucleotides or sequences involved in functions that are vital for in planta infection.
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Affiliation(s)
- Angel Y. S. Chen
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - James H. C. Peng
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - MaryLou Polek
- National Clonal Germplasm Repository for Citrus & DatesUSDA ARSRiversideCaliforniaUSA
| | - Tongyan Tian
- California Department of Food and AgricultureSacramentoCaliforniaUSA
| | - Márta Ludman
- Agricultural Biotechnology InstituteNational Research and Innovation CenterHungary
| | - Károly Fátyol
- Agricultural Biotechnology InstituteNational Research and Innovation CenterHungary
| | - James C. K. Ng
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
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Sanfaçon H. Modulation of disease severity by plant positive-strand RNA viruses: The complex interplay of multifunctional viral proteins, subviral RNAs and virus-associated RNAs with plant signaling pathways and defense responses. Adv Virus Res 2020; 107:87-131. [PMID: 32711736 DOI: 10.1016/bs.aivir.2020.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant viruses induce a range of symptoms of varying intensity, ranging from severe systemic necrosis to mild or asymptomatic infection. Several evolutionary constraints drive virus virulence, including the dependence of viruses on host factors to complete their infection cycle, the requirement to counteract or evade plant antiviral defense responses and the mode of virus transmission. Viruses have developed an array of strategies to modulate disease severity. Accumulating evidence has highlighted not only the multifunctional role that viral proteins play in disrupting or highjacking plant factors, hormone signaling pathways and intracellular organelles, but also the interaction networks between viral proteins, subviral RNAs and/or other viral-associated RNAs that regulate disease severity. This review focusses on positive-strand RNA viruses, which constitute the majority of characterized plant viruses. Using well-characterized viruses with different genome types as examples, recent advances are discussed as well as knowledge gaps and opportunities for further research.
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Affiliation(s)
- Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada.
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Harper SJ, Cowell SJ, Dawson WO. Isolate fitness and tissue-tropism determine superinfection success. Virology 2017; 511:222-228. [PMID: 28888112 DOI: 10.1016/j.virol.2017.08.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/24/2017] [Accepted: 08/26/2017] [Indexed: 01/07/2023]
Abstract
The mechanism of cross-protection, the deliberate infection of plants with a "mild" virus isolate to protect against "severe" isolates, has long been a topic of debate. In our model system, Citrus tristeza virus (CTV), this appears to be genotype-specific superinfection-exclusion, suggesting a simple recipe for cross-protection. However, this concept failed in field trials, which led us to examine the process of superinfection-exclusion more closely. We found that exclusion relies on the relative fitness of the primary versus the challenge isolates, and the host infected, and that significant differences in superinfection success could occur between isolates that differ by as few as 3 nucleotides. Furthermore, we found that exclusion was not uniform throughout the plant, but was tissue-specific. These data suggest that cross-protection is not a simple like-for-like process but a complex interaction between the primary and challenge isolates and the host.
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Affiliation(s)
- S J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, USA.
| | - S J Cowell
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA
| | - W O Dawson
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA
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Ziebell H, MacDiarmid R. Prospects for engineering and improvement of cross-protective virus strains. Curr Opin Virol 2017; 26:8-14. [PMID: 28743041 DOI: 10.1016/j.coviro.2017.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/21/2017] [Indexed: 11/17/2022]
Abstract
Mild strain cross-protection is currently an important method for the production of high quality plant products; despite challenge from severe virus isolates the initial protecting strain precludes symptom development. The mechanism of cross-protection is not yet resolved as RNA silencing does not sufficiently explain the phenomenon. Six requirements have been put forward to ensure long-lasting protection. We propose two additional requirements for effective and durable mild strain cross-protection; mild strains based on knowledge of the mechanism and consideration of impacts to consumers. Future research on predicting phenotype from genotype and understanding virus-plant and virus-vector interactions will enable improvement of cross-protective strains. Shared international databases of whole ecosystem interactions across a wide range of virus patho- and symbiotic-systems will form the basis for making step-change advances towards our collective ability to engineer and improve mild strain cross-protection.
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Affiliation(s)
- Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Messeweg 11-12, 38104 Braunschweig, Germany.
| | - Robin MacDiarmid
- New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, New Zealand
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Multiple viral infections in Agaricus bisporus - Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing. Sci Rep 2017; 7:2469. [PMID: 28550284 PMCID: PMC5446422 DOI: 10.1038/s41598-017-01592-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/29/2017] [Indexed: 12/16/2022] Open
Abstract
Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3′ motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interactive viral ecosystem with sequence variability ranging over 2 orders of magnitude and evidence of recombination, horizontal gene transfer and variable fragment numbers. Large numbers of viral RNAs were detected in multiple Agaricus samples; up to 24 in samples symptomatic for disease and 8–17 in asymptomatic samples, suggesting adaptive strategies for co-existence. The viral composition of growing cultures was dynamic, with evidence of gains and losses depending on the environment and included new hypothetical viruses when compared with the current transcriptome and EST databases. As the non-cellular transmission of mycoviruses is rare, the founding infections may be ancient, preserved in wild Agaricus populations, which act as reservoirs for subsequent cell-to-cell infection when host populations are expanded massively through fungiculture.
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Understanding superinfection exclusion by complex populations of Citrus tristeza virus. Virology 2016; 499:331-339. [DOI: 10.1016/j.virol.2016.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/28/2016] [Accepted: 10/01/2016] [Indexed: 12/20/2022]
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Some like it hot: citrus tristeza virus strains react differently to elevated temperature. Arch Virol 2016; 161:3567-3570. [DOI: 10.1007/s00705-016-3083-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
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Read DA, Pietersen G. PCR bias associated with conserved primer binding sites, used to determine genotype diversity within Citrus tristeza virus populations. J Virol Methods 2016; 237:107-113. [PMID: 27599411 DOI: 10.1016/j.jviromet.2016.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 01/07/2023]
Abstract
Citrus tristeza virus (CTV) is present in almost all of the major citrus production areas where it continues to reduce the profitability of citriculture. The accurate characterisation of CTV populations, which are usually made up of a number of disparate strains, requires the use of robust PCR protocols. Mismatches between primers and their corresponding binding sites may introduce primer-associated bias during amplification. The primer-associated bias of four sets of CTV specific primers, targeting the A and F regions and the p33 and p23 genes, were evaluated. This was done through the amplification of defined templates followed by their characterisation using the sequencing of multiple clones, as well as Illumina next generation sequencing. High levels of bias were found to be associated with the primer pairs targeting the A and F regions. The p33 gene primers were found to be biased against two genotypes and suggestions for preventing this apparent bias are discussed. The primer pair targeting the conserved p23 gene was found to have very little associated bias. Primers should undergo rigorous screening before being used to characterize virus populations that are known to exhibit high levels of variation, especially within primer binding sites.
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Affiliation(s)
- David Alan Read
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Gerhard Pietersen
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Agricultural Research Council-Plant Protection Research Institute, Pretoria 0002, South Africa.
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