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Karasev AV, Boyko VP, Gowda S, Nikolaeva OV, Hilf ME, Koonin EV, Niblett CL, Cline K, Gumpf DJ, Lee RF. Complete sequence of the citrus tristeza virus RNA genome. Virology 1995; 208:511-20. [PMID: 7747424 DOI: 10.1006/viro.1995.1182] [Citation(s) in RCA: 336] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The sequence of the entire genome of citrus tristeza virus (CTV), Florida isolate T36, was completed. The 19,296-nt CTV genome encodes 12 open reading frames (ORFs) potentially coding for at least 17 protein products. The 5'-proximal ORF 1a starts at nucleotide 108 and encodes a large polyprotein with calculated MW of 349 kDa containing domains characteristic of (from 5' to 3') two papain-like proteases (P-PRO), a methyltransferase (MT), and a helicase (HEL). Alignment of the putative P-PRO sequences of CTV with the related proteases of beet yellows closterovirus (BYV) and potyviruses allowed the prediction of catalytic cysteine and histidine residues as well as two cleavage sites, namely Val-Gly/Gly for the 5' proximal P-PRO domain and Met-Gly/Gly for the 5' distal P-PRO domain. The autoproteolytic cleavage of the polyprotein at these sites would release two N-terminal leader proteins of 54 and 55 kDa, respectively, and a 240-kDa C-terminal fragment containing MT and HEL domains. The apparent duplication of the leader domain distinguishes CTV from BYV and accounts for most of the size increase in the ORF 1a product of CTV. The downstream ORF 1b encodes a 57-kDa putative RNA-dependent RNA polymerase (RdRp), which is probably expressed via a +1 ribosomal frameshift. Sequence analysis of the frameshift region suggests that this +1 frameshift probably occurs at a rare arginine codon CGG and that elements of the RNA secondary structure are unlikely to be involved in this process. The complete polyprotein resulting from this frameshift event has a calculated MW of 401 kDa and after cleavage of the two N-terminal leaders would yield a 292-kDa protein containing the MT, HEL, and RdRp domains. Phylogenetic analysis of the three replication-associated domains, MT, HEL, and RdRp, indicates that CTV and BYV form a separate closterovirus lineage within the alpha-like supergroup of positive-strand RNA viruses. Two gene blocks or modules can be easily identified in the CTV genome. The first includes the replicative MT, HEL, and RdRp genes and is conserved throughout the entire alpha-like superfamily. The second block consists of five ORFs, 3 to 7, conserved among closteroviruses, including genes for the CTV homolog of HSP70 proteins and a duplicate of the coat protein gene. The 3'-terminal ORFs 8 to 11 encode a putative RNA-binding protein (ORF 11), and three proteins with unknown functions; this gene array is poorly conserved among closteroviruses.(ABSTRACT TRUNCATED AT 400 WORDS)
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Moreno P, Ambrós S, Albiach-Martí MR, Guerri J, Peña L. Citrus tristeza virus: a pathogen that changed the course of the citrus industry. MOLECULAR PLANT PATHOLOGY 2008; 9:251-68. [PMID: 18705856 PMCID: PMC6640355 DOI: 10.1111/j.1364-3703.2007.00455.x] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Citrus tristeza virus (CTV) (genus Closterovirus, family Closteroviridae) is the causal agent of devastating epidemics that changed the course of the citrus industry. Adapted to replicate in phloem cells of a few species within the family Rutaceae and to transmission by a few aphid species, CTV and citrus probably coevolved for centuries at the site of origin of citrus plants. CTV dispersal to other regions and its interaction with new scion varieties and rootstock combinations resulted in three distinct syndromes named tristeza, stem pitting and seedling yellows. The first, inciting decline of varieties propagated on sour orange, has forced the rebuilding of many citrus industries using tristeza-tolerant rootstocks. The second, inducing stunting, stem pitting and low bearing of some varieties, causes economic losses in an increasing number of countries. The third is usually observed by biological indexing, but rarely in the field. CTV polar virions are composed of two capsid proteins and a single-stranded, positive-sense genomic RNA (gRNA) of approximately 20 kb, containing 12 open reading frames (ORFs) and two untranslated regions (UTRs). ORFs 1a and 1b, encoding proteins of the replicase complex, are directly translated from the gRNA, and together with the 5' and 3'UTRs are the only regions required for RNA replication. The remaining ORFs, expressed via 3'-coterminal subgenomic RNAs, encode proteins required for virion assembly and movement (p6, p65, p61, p27 and p25), asymmetrical accumulation of positive and negative strands during RNA replication (p23), or suppression of post-transcriptional gene silencing (p25, p20 and p23), with the role of proteins p33, p18 and p13 as yet unknown. Analysis of genetic variation in CTV isolates revealed (1) conservation of genomes in distant geographical regions, with a limited repertoire of genotypes, (2) uneven distribution of variation along the gRNA, (3) frequent recombination events and (4) different selection pressures shaping CTV populations. Measures to control CTV damage include quarantine and budwood certification programmes, elimination of infected trees, use of tristeza-tolerant rootstocks, or cross protection with mild isolates, depending on CTV incidence and on the virus strains and host varieties predominant in each region. Incorporating resistance genes into commercial varieties by conventional breeding is presently unfeasible, whereas incorporation of pathogen-derived resistance by plant transformation has yielded variable results, indicating that the CTV-citrus interaction may be more specific and complex than initially thought. A deep understanding of the interactions between viral proteins and host and vector factors will be necessary to develop reliable and sound control measures.
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Folimonova SY, Robertson CJ, Garnsey SM, Gowda S, Dawson WO. Examination of the responses of different genotypes of citrus to huanglongbing (citrus greening) under different conditions. PHYTOPATHOLOGY 2009; 99:1346-54. [PMID: 19900000 DOI: 10.1094/phyto-99-12-1346] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
ABSTRACT Citrus Huanglongbing (HLB) is one of the most devastating diseases of citrus worldwide. The causal agent of HLB in Florida is thought to be 'Candidatus Liberibacter asiaticus'. In this work, we examined the responses of 30 different genotypes of citrus to Florida isolates of 'Ca. L. asiaticus' under controlled conditions in the greenhouse or growth room. Although 'Ca. L. asiaticus' was able to multiply in all of the plants, a wide range of responses was observed among different hosts. Based on the symptoms developed and the ability of plants to continue growth, the different genotypes were grouped into four categories: sensitive, which exhibited severe chlorosis on leaves, greatly reduced growth, and eventual death; moderately tolerant, which exhibited some scattered distinct symptoms but little or no growth reduction and no plant death; tolerant, which exhibited very minimal symptoms; and genotypes, which exhibited variable reactions. Interestingly, although 'Ca. L. asiaticus' was unevenly distributed within each particular plant, comparison of titers of the bacterium in different citrus genotypes revealed that most accumulated similar levels of 'Ca. L. asiaticus', demonstrating that there is no strict correlation between bacterial titer and severity of disease. Incubation of infected plants in the growth room with continuous light greatly affected symptoms production by reducing the time before distinctive symptoms developed and significantly increasing severity of chlorosis of leaves of all citrus genotypes. These results provide additional evidence of the correlation between disruption of phloem translocation of carbohydrates during HLB infection and the appearance of chlorotic symptoms in leaves of infected trees. We also examined interaction between 'Ca. L. asiaticus' and Citrus tristeza virus, which usually occurs in trees that become infected with HLB, and found no synergistic effect of the two pathogens. We trust that observations reported here will provide reagents for further examination of the 'Ca. L. asiaticus'-citrus interaction to advance the understanding of how 'Ca. L. asiaticus' causes disease and to develop methods or trees to overcome the disease.
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Rubio L, Ayllón MA, Kong P, Fernández A, Polek M, Guerri J, Moreno P, Falk BW. Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol 2001; 75:8054-62. [PMID: 11483750 PMCID: PMC115049 DOI: 10.1128/jvi.75.17.8054-8062.2001] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2001] [Accepted: 05/18/2001] [Indexed: 11/20/2022] Open
Abstract
We examined the population structure and genetic variation of four genomic regions within and between 30 Citrus tristeza virus (CTV) isolates from Spain and California. Our analyses showed that most isolates contained a population of sequence variants, with one being predominant. Four isolates showed two major sequence variants in some genomic regions. The two major variants of three of these isolates showed very low nucleotide identity to each other but were very similar to those of other isolates, suggesting the possibility of mixed infections with two divergent isolates. Incongruencies of phylogenetic relationships in the different genomic regions and statistical analyses suggested that the genomes of some CTV sequence variants originated by recombination events between diverged sequence variants. No correlation was observed between geographic origin and nucleotide distance, and thus from a genetic view, the Spanish and Californian isolates analyzed here could be considered members of the same population.
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Hilf ME, Karasev AV, Pappu HR, Gumpf DJ, Niblett CL, Garnsey SM. Characterization of citrus tristeza virus subgenomic RNAs in infected tissue. Virology 1995; 208:576-82. [PMID: 7747429 DOI: 10.1006/viro.1995.1188] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Citrus tristeza virus (CTV) specific RNAs extracted from infected citrus tissue were analyzed by Northern blot hybridization. RNAs were characterized by size and identified using cDNA probes specific to nine open reading frames (ORFs) identified by the analysis of sequence obtained from cDNA clones of the T36 isolate of CTV. Sequence specific cDNA probes identified the genomic RNA as well as subgenomic RNAs representing the p33, p65, p61, p27, p25, p18, p13, p20, and p23 ORFs in extracts of total or double-stranded RNA (dsRNA) isolated from infected tissue. A probe derived from the 3' terminal ORF (p23) hybridized to each of these subgenomic RNAs, indicating that the RNAs are 3' coterminal. The relative amounts of the different subgenomic RNAs varied widely. The RNAs for the p20 and p23 ORFs were the most abundant and surpassed the amount of the p25 or capsid protein specific subgenomic RNA. The number and sizes of the CTV subgenomic RNAs were the same in total RNA and dsRNA preparations. Propagation of T36 in seven different citrus hosts did not alter the pattern of subgenomic RNAs.
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Mawassi M, Mietkiewska E, Gofman R, Yang G, Bar-Joseph M. Unusual sequence relationships between two isolates of citrus tristeza virus. J Gen Virol 1996; 77 ( Pt 9):2359-64. [PMID: 8811037 DOI: 10.1099/0022-1317-77-9-2359] [Citation(s) in RCA: 129] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The complete, 19,226 nt sequence of the RNA genome from VT, a seedling yellows strain of citrus tristeza virus (CTV), was determined and found to have a genome organization identical with that of the previously determined CTV-T36 isolate, except that ORF 1 of CTV-VT was 70 nt shorter due to two widely separated 18 nt deletions. Sequence comparison of CTV-VT and CTV-T36 revealed approximately 89% identity throughout the ten 3' ORFs, but only 60-70% identity throughout ORF 1. The 5' nontranslated regions were only 60% identical whereas the 3' nontranslated regions were 97% identical. The transition between regions of similarity and deviation was gradual, suggesting that the sequence similarities and differences compared to CTV-T36 were unlikely to have arisen from a recent recombination event between a close T36 relative and a distantly related CTV isolate. This is the first attempt to compare in detail the variation between the genomes of two strains of a member of the closterovirus group. The observed deviation between the large RNA genomes of the two CTV strains is greater than that among different viruses of most other groups, raising the question of how to define the taxonomy of these viruses.
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Vives MC, Rubio L, L Pez C, Navas-Castillo J, Albiach-Mart MR, Dawson WO, Guerri J, Flores R, Moreno P. The complete genome sequence of the major component of a mild citrus tristeza virus isolate. J Gen Virol 1999; 80 ( Pt 3):811-816. [PMID: 10092023 DOI: 10.1099/0022-1317-80-3-811] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genome of the Spanish mild isolate T385 of citrus tristeza virus (CTV) was completely sequenced and compared with the genomes of the severe isolates T36 (Florida), VT (Israel) and SY568 (California). The genome of T385 was 19,259 nt in length, 37 nt shorter than the genome of T36, and 33 and 10 nt longer than those of VT and SY568, respectively, but their organization was identical. T385 had mean nucleotide identities of 81.3, 89.3 and 94% with T36, VT and SY568, respectively. The 3' UTR had over 97% identity in all isolates, whereas the 5' UTR of T385 had 67% identity with VT, 66.3% with SY568 and only 42.5% with T36. In the coding regions, the nucleotide differences between T385 and VT were evenly distributed along the genome (around 90% identity); this was not observed between T385 and the other isolates. T385 and T36 had nucleotide identities around 90% in the eight 3'-terminal ORFs of the genome, but only 72.3% in ORF 1a, a divergence pattern similar to that reported previously for T36 and VT. T385 and SY568 had nucleotide identities close to 90% in the 5'- and 3'-terminal regions of the genome, whereas the central region had over 99% identity. Our data suggest that the central region in the SY568 genome results from RNA recombination between two CTV genomes, one of which was almost identical to T385.
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Albiach-Martí MR, Mawassi M, Gowda S, Satyanarayana T, Hilf ME, Shanker S, Almira EC, Vives MC, López C, Guerri J, Flores R, Moreno P, Garnsey SM, Dawson WO. Sequences of Citrus tristeza virus separated in time and space are essentially identical. J Virol 2000; 74:6856-65. [PMID: 10888625 PMCID: PMC112203 DOI: 10.1128/jvi.74.15.6856-6865.2000] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first Citrus tristeza virus (CTV) genomes completely sequenced (19.3-kb positive-sense RNA), from four biologically distinct isolates, are unexpectedly divergent in nucleotide sequence (up to 60% divergence). Understanding of whether these large sequence differences resulted from recent evolution is important for the design of disease management strategies, particularly the use of genetically engineered mild (essentially symptomless)-strain cross protection and RNA-mediated transgenic resistance. The complete sequence of a mild isolate (T30) which has been endemic in Florida for about a century was found to be nearly identical to the genomic sequence of a mild isolate (T385) from Spain. Moreover, samples of sequences of other isolates from distinct geographic locations, maintained in different citrus hosts and also separated in time (B252 from Taiwan, B272 from Colombia, and B354 from California), were nearly identical to the T30 sequence. The sequence differences between these isolates were within or near the range of variability of the T30 population. A possible explanation for these results is that the parents of isolates T30, T385, B252, B272, and B354 have a common origin, probably Asia, and have changed little since they were dispersed throughout the world by the movement of citrus. Considering that the nucleotide divergence among the other known CTV genomes is much greater than those expected for strains of the same virus, the remarkable similarity of these five isolates indicates a high degree of evolutionary stasis in some CTV populations.
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Navas-Castillo J, Albiach-Martí MR, Gowda S, Hilf ME, Garnsey SM, Dawson WO. Kinetics of accumulation of citrus tristeza virus RNAs. Virology 1997; 228:92-7. [PMID: 9024813 DOI: 10.1006/viro.1996.8369] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Citrus tristeza virus (CTV), a member of the closterovirus group, is one of the more complex single-stranded RNA viruses. The 5' portion of its 19,296-nt, single-stranded RNA genome is expressed as an approximately 400-kDa polyprotein that is proteolytically processed, while the 10 3' open reading frames are expressed from 3'-coterminal subgenomic RNAs (sg RNAs). As an initial examination of the gene expression of this virus, we found that the kinetics of accumulation of genomic and sg RNAs and coat protein of the T36 isolate of CTV were similar in protoplasts of the natural host, citrus, and the experimental nonhost Nicotiana benthamiana. Newly synthesized genomic RNA was detected 2 days postinoculation and increased to a maximum at 3-5 days. The RNA complementary to the full-length virion RNA increased with similar kinetics, but at approximately one-tenth the concentration of genomic plus strands. Most of the abundant sg RNAs also accumulated in parallel to that of the genomic RNA. However, the smallest sg RNA, which corresponds to the p23 gene, increased earlier. The different sg RNAs accumulated in greatly differing amounts, in general with 3'-most sg RNAs accumulating to higher levels than 5' sg RNAs. However, some 3' sg RNAs (p13 and p18) accumulated to low levels. The two 3'-most sg RNAs (p23 and p20) accumulated to high levels approximately equal to that of the genomic RNA. The accumulation curve for coat protein paralleled that of its mRNA, suggesting that its regulation was transcriptional. Progeny virions from protoplasts were used to sequentially infect new protoplasts, serving as a potential source of virus that could evolve free from the genetic selection in intact plants for aphid transmission and movement.
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Locali-Fabris EC, Freitas-Astúa J, Souza AA, Takita MA, Astúa-Monge G, Antonioli-Luizon R, Rodrigues V, Targon MLPN, Machado MA. Complete nucleotide sequence, genomic organization and phylogenetic analysis of Citrus leprosis virus cytoplasmic type. J Gen Virol 2006; 87:2721-2729. [PMID: 16894213 DOI: 10.1099/vir.0.82038-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete nucleotide sequence of the genomic RNA 1 (8745 nt) and RNA 2 (4986 nt) of Citrus leprosis virus cytoplasmic type (CiLV-C) was determined using cloned cDNA. RNA 1 contains two open reading frames (ORFs), which correspond to 286 and 29 kDa proteins. The 286 kDa protein is a polyprotein putatively involved in virus replication, which contains four conserved domains: methyltransferase, protease, helicase and polymerase. RNA 2 contains four ORFs corresponding to 15, 61, 32 and 24 kDa proteins, respectively. The 32 kDa protein is apparently involved in cell-to-cell movement of the virus, but none of the other putative proteins exhibit any conserved domain. The 5′ regions of the two genomic RNAs contain a ‘cap’ structure and poly(A) tails were identified in the 3′-terminals. Sequence analyses and searches for structural and non-structural protein similarities revealed conserved domains with members of the genera Furovirus, Bromovirus, Tobravirus and Tobamovirus, although phylogenetic analyses strongly suggest that CiLV-C is a member of a distinct, novel virus genus and family, and definitely demonstrate that it does not belong to the family Rhabdoviridae, as previously proposed. Based on these results it was proposed that Citrus leprosis virus be considered as the type member of a new genus of viruses, Cilevirus.
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Visvader JE, Gould AR, Bruening GE, Symons RH. Citrus exocortis viroid: nucleotide sequence and secondary structure of an Australian isolate. FEBS Lett 2005; 137:288-92. [PMID: 15768484 DOI: 10.1016/0014-5793(82)80369-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Research Support, Non-U.S. Gov't |
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Kong P, Rubio L, Polek M, Falk BW. Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates. Virus Genes 2000; 21:139-45. [PMID: 11129629 DOI: 10.1023/a:1008198311398] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Closterovirus, Citrus tristeza virus (CTV) is an aphid-borne RNA virus that is the causal agent of important worldwide economic losses in citrus. Biological and molecular variation has been observed for many CTV isolates. In this work we detected and analyzed sequence variants (haplotypes) within individual CTV isolates. We studied the population structure of five California CTV isolates by single strand conformation polymorphism (SSCP) analysis of four CTV genomic regions. Also, we estimated the genetic diversity within and between isolates by analysis of haplotype nucleotide sequences. Most CTV isolates were composed of a population of genetically related variants (haplotypes), one being predominant. However in one case, we found a high nucleotide divergence between haplotypes of the same isolate. Comparison of these haplotypes with those from other isolates suggests that some CTV isolates could have arisen as result of a mixed infection of two divergent isolates.
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Satyanarayana T, Bar-Joseph M, Mawassi M, Albiach-Martí MR, Ayllón MA, Gowda S, Hilf ME, Moreno P, Garnsey SM, Dawson WO. Amplification of Citrus tristeza virus from a cDNA clone and infection of citrus trees. Virology 2001; 280:87-96. [PMID: 11162822 DOI: 10.1006/viro.2000.0759] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isolates of the Closterovirus, Citrus tristeza virus (CTV), are populations of disparate genotypes and defective RNAs developed during long periods of vegetative propagation of citrus trees. Because it has not been possible to obtain pure cultures of the virus, it is not known what components of the population are primarily responsible for induction of diseases. We previously developed an infectious cDNA clone from which in vitro-produced RNA transcripts could infect protoplasts (Satyanarayana et al., 1999, Proc. Natl. Acad. Sci. USA 96, 7433-7438). However, neither the RNA transcripts nor virions from transcript-infected protoplasts were competent for infection of citrus trees. Using a green fluorescent protein-marked virus as inoculum, we found that the approximately 20-kb RNA from virions or transcripts of cDNA infected only a small percentage of protoplasts ( approximately 0.01%), but virions could infect more than 80% of the protoplasts. Based on this information, we amplified the virus from the cDNA clone (recombinant virus) by successive passages in protoplasts using virions in crude sap as inoculum. By the third to seventh passages in protoplasts, maximal amounts of recombinant progeny virus were produced, which were used for inoculation of small citrus trees by slashing stems in the presence of virion preparations. A relatively high percentage of plants became infected with the recombinant virus from protoplasts, resulting in the first defined pure culture of CTV in plants. The comparative biology of the pure culture of recombinant CTV with that of the parental population in planta demonstrated that the recombinant virus retained through all of the recombinant DNA manipulations the normal functions of replication, movement, and aphid transmissibility, and had a symptom phenotype indistinguishable from that of the parental population. Additionally, fulfilling Koch's postulates of the first pure culture of CTV in plants suggested that the major genotype of the CTV T36 population is the primary determinant of the symptom phenotype. We could distinguish no biological contributions resulting from the minor genotypes and defective RNAs of the parental population.
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Cambra M, Gorris MT, Marroquín C, Román MP, Olmos A, Martínez MC, de Mendoza AH, López A, Navarro L. Incidence and epidemiology of Citrus tristeza virus in the Valencian community of Spain. Virus Res 2000; 71:85-95. [PMID: 11137164 DOI: 10.1016/s0168-1702(00)00190-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The first outbreak of citrus tristeza disease in Spain caused by Citrus tristeza virus (CTV) was recorded in 1957 in the Valencian Community (VC). In total c. 40 million trees, mainly of sweet orange and mandarin grafted on sour orange rootstocks, declined due to CTV. Large-scale surveys in different municipalities of the VC indicated that the disease spread very fast. Incidence increased from 11% in 1989 to 53% in 1998. Toxoptera aurantii and Aphis spiraecola (inefficient aphid vectors of CTV) predominated before 1985-87. Since then the relatively efficient vector Aphis gossypii has become dominant and induced an epidemic that has been modelled. The large number of A.gossypii that visited each clementine tree (estimated to exceed 97000 per year) explained the difference between the temporal pattern of spread of CTV in clementine which followed the Gompertz model and that in sweet orange (logistic model). The susceptibility of the different citrus species to CTV infection by aphids seems to depend on the number of young, succulent shoots produced. The epidemiological data allowed specific recommendations to be made to growers in order to facilitate a change to a modern citrus industry based on the use of selected varieties grafted on tristeza-tolerant rootstocks produced within a certification scheme. This has been done already in almost 90% of the VC citrus-growing area. The tristeza problem has been solved unless more aggressive isolates are introduced and become prevalent.
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Review |
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66 |
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Yang ZN, Mathews DM, Dodds JA, Mirkov TE. Molecular characterization of an isolate of citrus tristeza virus that causes severe symptoms in sweet orange. Virus Genes 1999; 19:131-42. [PMID: 10541017 DOI: 10.1023/a:1008127224147] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complete sequence (19,249 nucleotides) of the genome of citrus tristeza virus (CTV) isolate SY568 was determined. The genome organization is identical to that of the previously determined CTV-T36 and CTV-VT isolates. Sequence comparisons revealed that CTV-SY568, a severe stem-pitting isolate from California, has more than 87% overall sequence identity with CTV-VT, a seedling yellows isolate from Israel. Although SY568 has an overall sequence identity of 81% with CTV-T36, a quick decline isolate from Florida, the sequence identity in the 3' half of the genome is over 90% while the sequence identity in the 5' half of the genome is as low as 56%. Based on the sequence alignments of these three isolates, sequences in the 3' half of the genome are generally well conserved, while the sequences in the 5' half are relatively divergent. Sequence data of independent overlapping clones from the CTV-SY568 genome revealed two regions with highly divergent sequences. In open reading frame 1b (RNA dependent RNA polymerase), there were 118 nucleotide differences that lead to 16 amino acid changes. In the open reading frame of the divergent coat protein gene, 5 amino acid changes result from 48 nucleotide differences. Most differences occurred in the third position of the codons, and resulted in silent amino acid substitutions. RNase protection assays demonstrated that most of the clones obtained are representative of the major RNA species of this isolate. Northern analysis indicated that CTV-SY568 accumulated more viral RNA including genomic and certain subgenomic RNAs than isolates VT or T36 in sweet orange.
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Ito T, Ieki H, Ozaki K. Simultaneous detection of six citrus viroids and Apple stem grooving virus from citrus plants by multiplex reverse transcription polymerase chain reaction. J Virol Methods 2002; 106:235-9. [PMID: 12393154 DOI: 10.1016/s0166-0934(02)00147-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We developed a multiplex reverse transcription polymerase chain reaction (RT-PCR) to detect six citrus viroids: Citrus exocortis viroid (CEVd), Citrus bent leaf viroid (CBLVd), Hop stunt viroid (HSVd), Citrus viroid III (CVd-III), Citrus viroid IV (CVd-IV) and Citrus viroid OS (CVd-OS) and Apple stem grooving virus (ASGV, synonym: Citrus tatter leaf virus (CTLV)) from citrus plants. The multiplex RT-PCR was also designed to distinguish CVd-I-LSS (a distinct variant of CBLVd) from CBLVd. By the multiplex RT-PCR, one to eight fragments specific to the pathogens were simultaneously amplified from one sample and identified by their specific molecular sizes in 6% polyacrylamide gel electrophoresis. The results of the multiplex RT-PCR were consistent with those of other diagnoses, such as uniplex RT-PCR, to detect each of the pathogens. The multiplex RT-PCR provides a simple and rapid method for detecting various viroids and ASGV in citrus plants, which will help diagnose many citrus plants at a time.
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López C, Navas-Castillo J, Gowda S, Moreno P, Flores R. The 23-kDa protein coded by the 3'-terminal gene of citrus tristeza virus is an RNA-binding protein. Virology 2000; 269:462-70. [PMID: 10753724 DOI: 10.1006/viro.2000.0235] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 23-kDa protein (p23), encoded by the 3'-proximal gene of the RNA of Citrus tristeza virus (CTV), was overexpressed in Escherichia coli fused to the maltose-binding protein and purified by affinity chromatography. Gel retardation and UV crosslinking assays demonstrated that p23 has the ability to cooperatively bind single-stranded RNA in a non-sequence-specific manner. Formation of the p23-RNA complex was dependent on the conformational state of p23 and on the presence of a basic region, but the complex was stable at high salt concentrations, suggesting that interactions other than those between the negatively charged RNA and the basic region of p23 are involved. Competition assays showed that the affinity of p23 for single-stranded and double-stranded RNA was similar but considerably higher than for single-stranded and double-stranded DNA. By use of a series of artificially generated mutants, the RNA-binding domain of p23 was mapped between positions 50-86, a region containing several basic amino acids and a putative zinc-finger domain. Additional p23-derivatives lacking the conserved residues presumably involved in coordinating the zinc ion showed RNA-binding activity, but with an apparent dissociation constant higher than the wild-type protein. These conserved residues might confer binding specificity or increase binding stability in vivo. Within the Closteroviridae family, p23 is the only protein characterized so far showing RNA-binding activity.
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Reanwarakorn K, Semancik JS. Regulation of pathogenicity in hop stunt viroid-related group II citrus viroids. J Gen Virol 1998; 79 ( Pt 12):3163-71. [PMID: 9880036 DOI: 10.1099/0022-1317-79-12-3163] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleotide sequences were determined for two hop stunt viroid-related Group II citrus viroids characterized as either a cachexia disease non-pathogenic variant (CVd-IIa) or a pathogenic variant (CVd-IIb). Sequence identity between the two variants of 95.6% indicated a conserved genome with the principal region of nucleotide difference clustered in the variable (V) domain. Full-length viroid RT-PCR cDNA products were cloned into plasmid SP72. Viroid cDNA clones as well as derived RNA transcripts were transmissible to citron (Citrus medica L.) and Luffa aegyptiaca Mill. To determine the locus of cachexia pathogenicity as well as symptom expression in Luffa, chimeric viroid cDNA clones were constructed from segments of either the left terminal, pathogenic and conserved (T1-P-C) domains or the conserved, variable and right terminal (C-V-T2) domains of CVd-IIa or CVd-IIb in reciprocal exchanges. Symptoms induced by the various chimeric constructs on the two bioassay hosts reflected the differential response observed with CVd-IIa and -IIb. Constructs with the C-V-T2 domains region from clone-IIa induced severe symptoms on Luffa typical of CVd-IIa, but were non-symptomatic on mandarin as a bioassay host for the cachexia disease. Constructs with the same region (C-V-T2) from the clone-IIb genome induced only mild symptoms on Luffa, but produced a severe reaction on mandarin, as observed for CVd-IIb. Specific site-directed mutations were introduced into the V domain of the CVd-IIa clone to construct viroid cDNA clones with either partial or complete conversions to the CVd-IIb sequence. With the introduction of six site-specific changes into the V domain of the clone-IIa genome, cachexia pathogenicity was acquired as well as a moderation of severe symptoms on Luffa.
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Vives MC, Rubio L, Sambade A, Mirkov TE, Moreno P, Guerri J. Evidence of multiple recombination events between two RNA sequence variants within a Citrus tristeza virus isolate. Virology 2005; 331:232-7. [PMID: 15629767 DOI: 10.1016/j.virol.2004.10.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 08/23/2004] [Accepted: 10/21/2004] [Indexed: 10/26/2022]
Abstract
Analysis of sequence variants of a natural Citrus tristeza virus (CTV) isolate (SY568) revealed that its population was composed of three sequence types: (I) the most frequent type had > or =97.9% nucleotide identity with the sequence predominant in severe CTV isolates from different origins; (II) a second variant, genetically close to the major component of several mild isolates, had < or =85% identity with the first; and (III) several variants (less than 4%) resulted from homologous recombination at one or more sites between sequences I and II. Recombination sites had an AU-rich stretch of 8-89 nucleotides shared by both parental sequences, flanked by GC- and AU-rich regions upstream and downstream, respectively. This context has been suggested as a hot-spot for homologous recombination in other RNA viruses.
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Research Support, Non-U.S. Gov't |
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Mawassi M, Karasev AV, Mietkiewska E, Gafny R, Lee RF, Dawson WO, Bar-Joseph M. Defective RNA molecules associated with citrus tristeza virus. Virology 1995; 208:383-7. [PMID: 11831725 DOI: 10.1006/viro.1995.1165] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Preparations of single-stranded (ss) RNA extracted from particles of the Israeli VT strain of citrus tristeza virus (CTV-VT), and ss- and double-stranded (ds) RNA preparations extracted from infected Alemow (Citrus macrophylla) plants, contained a population of molecules with features that suggest that they are defective RNAs. The prototype of 2424 nt was cloned and sequenced and was found to be composed of two genomic regions corresponding to the 5' (1151 nt) and the 3' (1259 nt) termini of the genomic CTV-RNA, with two perfect direct repeats of eight nucleotides of unknown origin at the junction site. Northern hybridization analysis demonstrated that this 2.4-kb defective RNA is an abundant species among the other CTV-specific ss- and ds-RNAs in infected plants. The 2.4-kb RNA was found encapsidated by the CTV coat protein indicating that the CTV origin of assembly is located close to the 5' or 3' terminus. This is the first defective RNA to be reported for a member of the closterovirus group.
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Navarro B, Minutolo M, De Stradis A, Palmisano F, Alioto D, Di Serio F. The first phlebo-like virus infecting plants: a case study on the adaptation of negative-stranded RNA viruses to new hosts. MOLECULAR PLANT PATHOLOGY 2018; 19:1075-1089. [PMID: 28752569 PMCID: PMC6637980 DOI: 10.1111/mpp.12587] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 05/07/2023]
Abstract
A novel negative-stranded (ns) RNA virus associated with a severe citrus disease reported more than 80 years ago has been identified. Transmission electron microscopy showed that this novel virus, tentatively named citrus concave gum-associated virus, is flexuous and non-enveloped. Notwithstanding, its two genomic RNAs share structural features with members of the genus Phlebovirus, which are enveloped arthropod-transmitted viruses infecting mammals, and with a group of still unclassified phlebo-like viruses mainly infecting arthropods. CCGaV genomic RNAs code for an RNA-dependent RNA polymerase, a nucleocapsid protein and a putative movement protein showing structural and phylogenetic relationships with phlebo-like viruses, phleboviruses and the unrelated ophioviruses, respectively, thus providing intriguing evidence of a modular genome evolution. Phylogenetic reconstructions identified an invertebrate-restricted virus as the most likely ancestor of this virus, revealing that its adaptation to plants was independent from and possibly predated that of the other nsRNA plant viruses. These data are consistent with an evolutionary scenario in which trans-kingdom adaptation occurred several times during the history of nsRNA viruses and followed different evolutionary pathways, in which genomic RNA segments were gained or lost. The need to create a new genus for this bipartite nsRNA virus and the impact of the rapid and specific detection methods developed here on citrus sanitation and certification are also discussed.
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Rodrigues JCV, Kitajima EW, Childers CC, Chagas CM. Citrus leprosis virus vectored by Brevipalpus phoenicis (Acari: Tenuipalpidae) on citrus in Brazil. EXPERIMENTAL & APPLIED ACAROLOGY 2003; 30:161-79. [PMID: 14756415 DOI: 10.1023/b:appa.0000006547.76802.6e] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Citrus leprosis is caused by Citrus leprosis virus (CiLV) that is transmitted by mites in the genus Brevipalpus (Acari: Tenuipalpidae). This disease directly reduces production and the life span of the citrus plant. The main symptoms of the disease include lesions on fruits, leaves, and twigs or small branches, causing premature fruit drop, defoliation, and death of the twigs or branches leading to serious tree decline. Leprosis is a highly destructive disease of citrus, wherever it occurs. The Brazilian citrus industry spends over 100 million US dollars annually on acaricides to control the vector, Brevipalpus phoenicis (Geijskes). This review contains information about the history of the etiology of citrus leprosis, its geographical distribution, host range, the role of the mite vectors, viral morphology and relationships with the infected cell, and transmissibility of the virus by the mite. In addition, data on the mite-virus-plant relationship, disease damage, and strategies for controlling disease spread are presented.
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Mawassi M, Mietkiewska E, Hilf ME, Ashoulin L, Karasev AV, Gafny R, Lee RF, Garnsey SM, Dawson WO, Bar-Joseph M. Multiple species of defective RNAs in plants infected with citrus tristeza virus. Virology 1995; 214:264-8. [PMID: 8525626 DOI: 10.1006/viro.1995.9930] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Alemow (Citrus macrophylla) and sweet orange (C. sinensis) plants infected, respectively, with several Israeli and Florida isolates of the citrus tristeza virus (CTV) were found to contain multiple species of RNA molecules with features similar to defective-interfering RNAs. Northern blot hybridizations of dsRNAs extracted from serial passages of the Israeli VT isolate (CTV-VT) and from different plants infected with a single source of inoculum showed considerable variation both in the presence and in the relative abundance of the defective RNA (D-RNA) bands. The D-RNA molecules were found to be encapsidated in the CTV particles. Sequence analysis of two VT D-RNA molecules of 2.7 and 4.5 kb revealed that they were composed of two regions corresponding to 1818 and 4036 nucleotides from the 5' and 938 and 442 nucleotides from the 3' termini of the CTV-VT genomic RNA, respectively. A short (ca. 0.8 kb) nonencapsidated single-stranded positive-sense RNA species was also found in infected plants. This ssRNA, which copurified with dsRNAs, was shown by hybridization to encompass the 5'-terminal part of the CTV genome and might have an extensive secondary structure.
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Roy A, Fayad A, Barthe G, Brlansky RH. A multiplex polymerase chain reaction method for reliable, sensitive and simultaneous detection of multiple viruses in citrus trees. J Virol Methods 2005; 129:47-55. [PMID: 15951030 DOI: 10.1016/j.jviromet.2005.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 04/20/2005] [Accepted: 05/09/2005] [Indexed: 11/28/2022]
Abstract
A multiplex polymerase chain reaction (mPCR) assay was developed to detect six RNA and one DNA citrus virus: Citrus leaf rugose virus (CLRV), Citrus psorosis virus (CPsV), Citrus tatter leaf virus (CTLV), Citrus tristeza virus (CTV), Citrus variegation virus (CVV), Citrus yellow mosaic virus (CYMV), and Indian citrus ringspot virus (ICRSV) from citrus plants. These seven viruses are classified in six different virus genera. Degenerate primers were designed based on the respective virus isolate sequence data available from the GenBank and were used for reliable detection of the different viruses by simplex- and mPCR. The sensitive and simultaneous detection of RNA and DNA viruses using the mPCR decreases the risk of contamination, saves time and reduces the cost as compared to other conventional methods for citrus virus detection. Seven different fragments (245-942 bp) specific to the viruses were simultaneously amplified using mPCR and were identified on the basis of their molecular sizes. The consistent results of the mPCR were compared with simplex PCR for detection of each virus pathogen. The mPCR results were confirmed with sequencing analysis. The mPCR provides a useful rapid method for detecting multiple viruses in citrus plants that will aid in the production of virus-free citrus plants for certification programs.
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Research Support, U.S. Gov't, Non-P.H.S. |
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Roy A, Choudhary N, Guillermo LM, Shao J, Govindarajulu A, Achor D, Wei G, Picton DD, Levy L, Nakhla MK, Hartung JS, Brlansky RH. A novel virus of the genus Cilevirus causing symptoms similar to citrus leprosis. PHYTOPATHOLOGY 2013; 103:488-500. [PMID: 23268581 DOI: 10.1094/phyto-07-12-0177-r] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Citrus leprosis in Colombia was previously shown to be caused by cytoplasmic Citrus leprosis virus (CiLV-C). In 2011, enzyme-linked immunosorbent assay and reverse-transcription polymerase chain reaction (RT-PCR)-based diagnostic methods failed to identify CiLV-C from citrus samples with symptoms similar to citrus leprosis; however, virions similar to CiLV-C were observed in the cytoplasm of the symptomatic leaves by transmission electron microscopy. Furthermore, the causal organism was transmitted by the false spider mite, Brevipalpus phoenicis, to healthy citrus seedlings. A library of small RNAs was constructed from symptomatic leaves and used as the template for Illumina high-throughput parallel sequencing. The complete genome sequence and structure of a new bipartite RNA virus was determined. RNA1 (8,717 nucleotides [nt]) contained two open reading frames (ORFs). ORF1 encoded the replication module, consisting of five domains: namely, methyltransferase (MTR), cysteine protease-like, FtsJ-MTR, helicase (Hel), and RNA-dependent RNA polymerase (RdRp); whereas ORF2 encoded the putative coat protein. RNA2 (4,989 nt) contained five ORFs that encode the movement protein (MP) and four hypothetical proteins (p7, p15, p24, and p61). The structure of this virus genome resembled that of CiLV-C except that it contained a long 3' untranslated terminal region and an extra ORF (p7) in RNA2. Both the RNA1 and RNA2 of the new virus had only 58 and 50% nucleotide identities, respectively, with known CiLV-C sequences and, thus, it appears to be a novel virus infecting citrus. Phylogenetic analyses of the MTR, Hel, RdRp, and MP domains also indicated that the new virus was closely related to CiLV-C. We suggest that the virus be called Citrus leprosis virus cytoplasmic type 2 (CiLV-C2) and it should be unambiguously classified as a definitive member of the genus Cilevirus. A pair of CiLV-C2 genome-specific RT-PCR primers was designed and validated to detect its presence in citrus leprosis samples collected from the Casanare and Meta states in Colombia.
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Comparative Study |
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