Russian Isolates of <i>Potato spindle tuber viroid</i> Exhibit Low Sequence Diversity

Owens, Robert A.; Girsova, N.V.; Kromina, K A; Lee, Ing Ming; Mozhaeva, K. A.; Kastalyeva, T. B.

doi:10.1094/pdis-93-7-0752

Cited by 17 publications

(6 citation statements)

References 20 publications

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“…PSTVd variants consisted of 356-359 nucleotides ( Table 2 ), and were much more diverse than TCDVd variants. One variant, which was designated variant I, showed 100% sequence identity with EF044303, a sequence obtained from the potato PSTVd isolate “Bugry-97” from Russia [ 32 ]. The rest exhibited 1 to 11 nucleotide differences from variant I/EF044303 ( Table 2 ).…”

Section: Resultsmentioning

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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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: 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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“…В бывшем СССР «готическая» болезнь картофеля, вызываемая вироидом веретеновидности клубнеи� картофеля, или ВВКК, впервые была зарегистрирована в начале 1930-х гг., а к концу 1980-х гг. ВВКК распространился в посадках картофеля в Центральном, Северо-Западном и Дальневосточном округах России� -скои� Федерации (Kastalyeva et al, 1992;Owens et al, 2009). ВВКК был обнаружен более чем в 50% меристемнои� культуры in vitro (Kastalyeva et al, 1992), а также у некоторых сортов картофеля в Приморском крае на Дальнем Востоке (Romanova et al, 2007).…”

Section: диагностика ввкк методом отпцр (пцр с обратной транскрипцией...unclassified

<i>Solanum nigrum</i> L. is a potato spindle tuber viroid reservoir

Мироненко

Хютти

Kyrova

et al. 2022

Trudy po prikladnoy botanike, genetike i selektsii

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Background. Among the weeds of the Solanaceae family, a potential viroid infection reservoir, black nightshade (Solanum nigrum L.), is ubiquitous in Russia.Materials and methods. Molecular diagnostics of the viroid was performed using RT-PCR with the P3/P4 primers specific for PSTVd and 6Pospi F/R specific for the Pospiviroidae family of viroids. The amplification products were cloned and sequenced, and the nucleotide sequences were deposited in the GenBank database.Results. RT-PCR showed that 80–100% of plants were infected with PSTVd. The cDNA amplicons of two plants from Nizhny Novgorod (Sn1 and Sn2) and one plant from Tula Province (Sn3) were cloned (3 clones each) and sequenced. An analysis of the nucleotide variability in the clones revealed significant genetic differences between the PSTVd strains, independent of the geographical origin. Mutations U120C and U192C, compared with the reference strain VP35 (LC523658), were found in all 9 clones. The Sn1 isolate was close to the “potato” VP35 isolate and differed from it only by three mutations. The Sn2 isolate was represented by three identical clones and differed from VP35 by nine mutations, while Sn3 had 22 mutations in the region of 49–310 nucleotide positions in total for three clones. After artificial infection of healthy S. nigrum plants in a greenhouse, the presence of PSTVd in infected plants was confirmed and it was proved that the viroid was transmitted by seeds to plants of the next generation.Conclusion. For the first time in externally healthy plants of S. nigrum, widely distributed in the potato fields of Russia (Nizhny Novgorod and Tula Province), the potato spindle tuber viroid, PSTVd, was detected. It was proved that the viroid was preserved in the seeds of S. nigrum and transmitted to their progeny. Genetic heterogeneity of PSTVd strains from S. nigrum plants was found. Two mutations, U120C and U192C, were common for all tested clones of PSTVd strains.

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“…The circular RNA was found to be composed of five functional/structural domains named Terminal left (TL), Pathogenicity (P), Central (C), Variable (V), and Terminal right (TR) [ 14 ]. So far, more than 300 PSTVd strains or variants have been reported, and numerous mutations have been identified throughout the genome; however, many of them are concentrated in the P and V domains [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. Analysis of mutations found in PSTVd isolates with different pathogenicity to tomato ( Solanum lycopersicum ) strongly supported the premise that nucleotide sequences or structures in the P domain play a major role in determining pathogenicity.…”

Section: Introductionmentioning

confidence: 99%

Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid

Kitabayashi

Tsushima

Adkar-Purushothama

et al. 2020

IJMS

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While the potato spindle tuber viroid (PSTVd) variant, PSTVd-Dahlia (PSTVd-D or PSTVd-Dwt) induces very mild symptoms in tomato cultivar ‘Rutgers’, PSTVd-Intermediate (PSTVd-I or PSTVd-Iwt) induces severe symptoms. These two variants differ by nine nucleotides, of which six mutations are located in the terminal left (TL) to the pathogenicity (P) domains. To evaluate the importance of mutations located in the TL to the P domains, ten types of point mutants were created by swapping the nucleotides between the two viroid variants. Bioassay in tomato plants demonstrated that two mutants created on PSTVd-Iwt at positions 42 and 64 resulted in symptom attenuation. Phenotypic and RT-qPCR analysis revealed that mutation at position 42 of PSTVd-Iwt significantly reduced disease severity and accumulation of the viroid, whereas mutation at position 64 showed a significant reduction in stunting when compared to the PSTVd-Iwt infected plant. RT-qPCR analysis on pathogenesis-related protein 1b1 and chalcone synthase genes showed a direct correlation with symptom severity whereas the expansin genes were down-regulated irrespective of the symptom severity. These results indicate that the nucleotides at positions 42 and 64 are in concert with the ones at positions 43, 310, and 311/312, which determines the slower and stable accumulation of PSTVd-D without eliciting excessive host defense responses thus contributing in the attenuation of disease symptom.

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Russian Isolates of Potato spindle tuber viroid Exhibit Low Sequence Diversity

Cited by 17 publications

References 20 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

<i>Solanum nigrum</i> L. is a potato spindle tuber viroid reservoir

Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid

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