Pear blister canker viroid: sequence variability and causal role in pear blister canker disease

Ambrós, Silvia; Desvignes, J.C.; Llácer, G.; Flores, Ricardo

doi:10.1099/0022-1317-76-10-2625

Cited by 23 publications

(17 citation statements)

References 17 publications

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“…For PSTVd, 8 sequence variants at occurrence frequencies ranging from 3.0% to 30.3% were found in clones obtained from PSTVd-infected plant 1; and 9 variants at occurrence frequencies of 3.4% to 44.8% in clones obtained from plant 2 (Table 2). These results demonstrate that TCDVd, like PSTVd as well as many other viroid species [19,21,22,23,24,25,26], exists as a collective group comprised of various sequence variants. Nevertheless, TCDVd was less diverse than PSTVd in tomato plants, as fewer TCDVd variants and lower haplotype diversity (0.500 and 0.499 for TCDVd vs. 0.799 and 0.697 for PSTVd) was observed in the clones from the plants (Table 1 and Table 2).…”

Section: Resultsmentioning

confidence: 69%

“…Members of the Pospiviroidae family replicate in the nucleus by host DNA-dependent RNA polymerase II [1]. The lack of proof-reading activity of the plant polymerase(s), the large population size, and the rapid rate of RNA replication have been suggested to result in genetic polymorphism, as demonstrated in various viroids including PSTVd [16,17,18], Citric exocortis viroid (CEVd) [19,20], Hop stunt viroid (HSVd) [21], Australian grapevine viroid (AGVd) [22], Pear blister canker viroid [23], Peach latent mosaic viroid (PLMVd) [24,25], Grapevine yellow speckle viroid- 1 (GYSVd-1) [26], and Chrysanthemum stunt viroid (CSVd) [27]. In this study, the genetic variants of TCDVd and PSTVd in tomato plants were investigated and analyzed.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

Nie

2012

Viruses

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The sequence polymorphism and population structure of Tomato chlorotic dwarf viroid (TCDVd) (isolate Trust) and Potato tuber spindle viroid (PSTVd) (isolate FN) in tomato plants were investigated. Of the 9 and 35 TCDVd clones sequenced from 2 different TCDVd-infected plants, 2 and 4 sequence variants were identified, respectively, leading to a total of 4 sequence variants of 360 nucleotides in length. Variant I was identical to AF162131, the first TCDVd sequence to be reported, and the rest exhibited 1 to 3 nucleotide differences, all in the TR domain, from AF162131/variant I. Of the 33 and 29 PSTVd clones sequenced from 2 different PSTVd-infected plants, 8 and 9 sequence variants were found, respectively, leading to a total of 15 variants ranging in length from 356 to 359 nucleotides. The variant I was identical to EF044303, a PSTVd reported in Russia. The rest exhibited 1 to 11 nucleotide differences scattering in all five domains from EF044303/variant I. The results demonstrated for the first time that TCDVd, like many other viroids including PSTVd, exists in host plants as a collective group comprised of various sequence variants. However, in comparison to PSTVd, TCDVd is less polymorphic in tomato plants as fewer variants and lower haplotype/nucleotide diversities were observed.

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Section: Resultsmentioning

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

Nie

2012

Viruses

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“…Many reports describe the characterization of viroid populations such as HSVd, CEVd, GYSVd1 and PLMVd [12][13][14][15][16][17][18][19][20], but this is the first report on the genetic diversity and phylogenetic analysis of AGVd. Here, a hundred of independent cDNA clones from each of the three isolates, in total of 300, were sequenced.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and phylogenetic analysis of Australian Grapevine Viroid (AGVd) isolated from different grapevines in China

Jiang

Peng

et al. 2008

Virus Genes

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Australian grapevine viroid (AGVd) is found in only three countries in the world. Here, the genetic diversity and phylogenetic relationships of AGVd isolates from three different grape varieties (Thomson Seedless, Jingchuan and Zaoyu) in China were studied. A hundred of independent cDNA clones from each of the three isolates, in total of 300, were sequenced. We identified 29 sequence variants including two predominant ones in Thomson Seedless, and 48 each including a unique predominant one in Jingchuan and Zaoyu. In silico structure analysis revealed that base changes were clustered in the left terminal domain of the predicted secondary structure in all three isolates. Further, these changes were shown to affect their secondary structures to varying degrees. Genetic diversity and phylogenetic analysis of four predominant sequence variants from this study, plus four others from Australia and Tunisia, revealed obvious regional disparity and variety-specificity in AGVd.

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“…Genetic recombination is an important process for eliminating detrimental mutations and ensuring greater genetic diversity. Recombination occurs in mixed infections of some closely related RNA viruses that encode their own RNA polymerases (30) and in viroids that are dependent on the cellular enzymatic activities for replication (1,4,14,23,24,43,47,52,54). However, although phylogenetic analysis suggests that genetic recombination can occur both between and within HDV genotypes (67), HDV recombinants have never been isolated from HDV mixed-genotype infections (66) either in nature or in the laboratory.…”

mentioning

confidence: 99%

RNA Recombination of Hepatitis Delta Virus in Natural Mixed-Genotype Infection and Transfected Cultured Cells

Wang

Chao

2005

J Virol

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Most RNA viruses encode their own RNA polymerases for genome replication, and increasing numbers of them appear to be capable of undergoing RNA recombination. Here, we provide the first report of intergenotypic recombination in hepatitis delta virus (HDV), the only animal RNA virus that requires host RNA polymerase(s) for viral replication. In vivo, we analyzed RNA species derived from the serum of a patient with mixed genotype I and genotype IIb HDV infection by using multiple restriction fragment length polymorphism (RFLP) assays and sequence analysis of cloned reverse transcription (RT)-PCR products. Six HDV recombinants were isolated from 101 tested clones, and HDV recombination in this patient was further confirmed by RT-PCR with genotype-specific primer pairs. Analysis of the recombination junctions suggested that the HDV genome rearrangement occurred through faithful homologous recombination. We then used an RNA cotransfection cell culture system to investigate HDV RNA recombination in vitro. We found that HDV recombinants could indeed be detected in the transfected cells; some of these possessed recombination junctions identical to those identified in vivo. Furthermore, using a PCR-independent RNase protection assay, we were able to readily identify the recombined HDV RNA species in cultured cells. Taken together, our results demonstrate that HDV RNA recombination occurs in both natural HDV infections and cultured cells, thereby presenting a novel mechanism for HDV evolution.Hepatitis delta virus (HDV) is a subviral agent of the hepatitis B virus that requires hepatitis B surface antigen for its assembly and transmission (48,49). HDV is unique among animal viruses in that it resembles some plant pathogens, such as viroids, in having a circular RNA with an unbranched rodlike structure (25, 59), and a replication strategy that utilizes host RNA polymerases (Pols) (37, 41). Upon entering a cell, genomic HDV RNA is transcribed into complementary subgenomic mRNA for the delta antigen (HDAg) (15) and multimeric antigenomic RNAs (31, 57). These then undergo selfcleavage and ligation to generate unit-length circular RNA (27,46,53,63). Similarly, the circular antigenomic RNA serves as a template for production of additional genomic RNA.In both virions and cells, the HDV RNA forms a ribonucleoprotein complex with HDAg (9, 35). There are two forms of HDAg, small and large, which play distinct biological roles. The small HDAg (195 amino acids) is required for HDV RNA replication (8,29). The large HDAg is produced through specific RNA editing by the small form of the cellular enzyme ADAR1 (20,44,62), which converts the UAG stop codon for the small HDAg into a UGG tryptophan codon (36). This process leads to translation of an additional 19 amino acids and creates the large HDAg (214 amino acids), which in turns inhibits genome replication and is required for packaging (6,8).Viral hepatitis due to HDV infection has been found worldwide, and the complete nucleotide (nt) sequences of HDV genomes have been reported from m...

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Pear blister canker viroid: sequence variability and causal role in pear blister canker disease

Cited by 23 publications

References 17 publications

Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

Genetic diversity and phylogenetic analysis of Australian Grapevine Viroid (AGVd) isolated from different grapevines in China

RNA Recombination of Hepatitis Delta Virus in Natural Mixed-Genotype Infection and Transfected Cultured Cells

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