Molecular sampling of hop stunt viroid (HSVd) from grapevines in hop production areas in the Czech Republic and hop protection

Matoušek, J.; Orctová, Lidmila; Patzak, Josef; Svoboda, P.; Ludvikova, Ivana

doi:10.17221/4109-pse

Cited by 20 publications

(9 citation statements)

References 26 publications

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“…HSVd was earlier detected in Czech grapevines by [39]. However, the samples tested in the study mentioned were taken in the vicinity of hops gardens in northern Bohemia and the Znojmo wine-producing region.…”

Section: Resultsmentioning

confidence: 94%

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

et al. 2016

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Comprehensive next generation sequencing virus detection was used to detect the whole spectrum of viruses and viroids in selected grapevines from the Czech Republic. The novel NGS approach was based on sequencing libraries of small RNA isolated from grapevine vascular tissues. Eight previously partially-characterized grapevines of diverse varieties were selected and subjected to analysis: Chardonnay, Laurot, Guzal Kara, and rootstock Kober 125AA from the Moravia wine-producing region; plus Müller-Thurgau and Pinot Noir from the Bohemia wine-producing region, both in the Czech Republic. Using next generation sequencing of small RNA, the presence of 8 viruses and 2 viroids were detected in a set of eight grapevines; therefore, confirming the high effectiveness of the technique in plant virology and producing results supporting previous data on multiple infected grapevines in Czech vineyards. Among the pathogens detected, the Grapevine rupestris vein feathering virus and Grapevine yellow speckle viroid 1 were recorded in the Czech Republic for the first time.

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Section: Resultsmentioning

confidence: 94%

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

et al. 2016

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“…HSVd was first discovered in Japanese hop fields, causing hop stunt disease, which appeared 3–5 years after infection as plant stunting, small cone formation and a substantial reduction of alpha-acid content [ 7 , 8 ]. The occurrence of this viroid, which is nowadays known to be commonly present in several woody hosts, including grapevine [ 9 ], was later also confirmed in other hop growing countries [ 10 – 12 ]. AFCVd symptoms on hop resemble those of HSVd, and it is currently restricted to Japan [ 13 ].…”

Section: Introductionmentioning

confidence: 85%

Development of hop transcriptome to support research into host-viroid interactions

et al. 2017

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Viroids, the smallest known pathogens, unable to encode any proteins, can cause severe diseases in their host plants. One of the proposed mechanisms of their pathogenicity includes silencing the host’s genes via viroid-derived small RNAs, which are products of the host’s immune response to the viroid’s double stranded RNA. Humulus lupulus (hop) plants are hosts to several viroids; two of them, HLVd and CBCVd, are interesting models for studying host-viroid interactions, due to the symptomless infection of the former and severe stunting disease caused by the latter. To study these interactions, we constructed a deep hop NGS transcriptome based on 35 Gb paired-end sequencing data assembled into over 74 Mb of contigs. These transcripts were used for in-silico prediction of target transcripts of vd-sRNA of the two aforementioned viroids, using two different software tools. Prediction models revealed that 1062 and 1387 hop transcripts share nucleotide similarities with HLVd- and CBCVd-derived small RNAs, respectively, so they could be silenced in an RNA interference process. Furthermore, we selected 17 transcripts from 4 groups of targets involved in the metabolism of plant hormones, small RNA biogenesis, transcripts with high complementarity with viroid-derived small RNAs and transcripts targeted by CBCVd-derived small RNAs with high cellular concentrations. Their expression was monitored by reverse transcription quantitative PCR performed using leaf, flower and cone samples. Additionally, the expression of 5 pathogenesis related genes was monitored. Expression analysis confirmed high expression levels of four pathogenesis related genes in leaves of HLVd and CBCVd infected hop plants. Expression fluctuations were observed for the majority of targets, with possible evidence of downregulation of GATA transcription factor by CBCVd- and of linoleate 13S-lipoxygenase by HLVd-derived small RNAs. These results provide a deep transcriptome of hop and the first insights into complex viroid-hop plant interactions.

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“…When analysing multiple forms of viroids, such as quasispecies, PAGE is not enough, so different variants of viroids need to be detected by thermodynamic methods, TGGE, and cDNA heteroduplex analysis or by cDNA cloning and sequencing. Some of these quasispecies analyses have been done for HSVd, HLVd and PSTVd (Matousek et al ., , , ).…”

Section: Methods For Viroid Detectionmentioning

confidence: 99%

Diagnostic techniques for viroids

et al. 2016

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The fast growth of the human population forces us to produce more food, but higher crop production also leads to the fast spread of diseases. Plant pathology deploys a wide range of methods that do not provide an adequate solution to all disease losses. In the case of viroids, therapeutic means of control are not available; therefore control strategies are more focused on the development of reliable detection methods to quickly exclude the infected plant material. Although viroids are the smallest and simplest plant pathogens, their identification and detection is not straightforward. Each viroid–host combination is specific, and for reliable identification, all steps from sampling to final detection must be performed accurately. In this review, several methods for viroid detection in various host plants are discussed, including their advantages and disadvantages. Even though relatively new molecular methods enable fast and sensitive detection of viroids, a combination of different methods gives the most reliable identification. Techniques based on nucleic acids may be the future for viroid detection but they still cannot replace biological indexing, which is usually essential in epidemiological and aetiological studies.

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Molecular sampling of hop stunt viroid (HSVd) from grapevines in hop production areas in the Czech Republic and hop protection

Cited by 20 publications

References 26 publications

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic)

Development of hop transcriptome to support research into host-viroid interactions

Diagnostic techniques for viroids

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