Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections

Czotter, Nikoletta; Molnár, J.; Pesti, Réka; Demián, Emese; Baráth, Dániel; Varga, Tünde; Várallyay, Éva

doi:10.1007/978-1-4939-7683-6_9

Cited by 18 publications

(20 citation statements)

References 15 publications

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“…Pools, representing the vineyards (1-19) were prepared with the same strategy by mixing equal amounts of RNA from all of the sampled plants. Small RNA libraries were prepared using a TruSeq Small RNA Library Preparation Kit (Illumina) and our in-house-modified protocol (Czotter et al 2018a). One sequencing library/plantation or collection were sequenced (19 in total) using a single index on a HiScanSQ by UD-Genomed (Debrecen, Hungary) (50bp, single-end sequencing, with 8 samples/sequencing lane).…”

Section: Plant Materials and Sample Preparationmentioning

confidence: 99%

Grapevine rootstocks can be a source of infection with non-regulated viruses

et al. 2020

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Grapevine can be infected by several viruses and viroids, the presence of which can lead to yield losses and vineyard decline. Our previous survey of vineyards in Hungary suggested that viral infection originates from infected propagation material. To investigate whether rootstocks can be a source of virus infections, we surveyed seventeen rootstock vineyards and two rootstock collections in Hungary to determine the virome by high-throughput sequencing of small RNAs. The presence of the viruses was also tested by RT-PCR. The results showed that viruses whose presence is routinely checked were almost absent in rootstock vineyards but were present in rootstock genotype collections. Moreover, first the time in Hungary, we detected the presence of Australian grapevine viroid in the rootstock genotype collection at Pecs. In contrast, viruses that are not regulated or not routinely tested, namely, grapevine rupestris stempitting-associated virus, grapevine Syrah virus-1 and grapevine Pinot gris virus, were detected in almost all locations in most of the varieties. The presence and absence of infected rootstock genotypes in the same vineyard together with phylogenetic analysis suggested that viral infections originated from infected propagation material. Moreover, we found the symptomatic variant of grapevine Pinot gris virus in several rootstock vineyards without symptoms, suggesting the possibility for leaf mottling and deformation disease symptoms to manifest on susceptible cultivars following grafting onto these rootstocks.

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Section: Plant Materials and Sample Preparationmentioning

confidence: 99%

Grapevine rootstocks can be a source of infection with non-regulated viruses

et al. 2020

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“…Leaf samples of the in vitro cultured plantlets from all three varieties were also collected. RNA was extracted from leaf samples by the CTAB method [ 42 ]. RNA pools, representing each variety at different locations (isolator house or stock nursery) were prepared by mixing equal amounts of RNA originating from different individuals.…”

Section: Methodsmentioning

confidence: 99%

“…RNA pools, representing each variety at different locations (isolator house or stock nursery) were prepared by mixing equal amounts of RNA originating from different individuals. These pools were used for sRNA library preparation (five libraries in total) using Truseq Small RNA Library Preparation Kit (Illumina, San Diego, CA, USA) and our modified protocol [ 42 ]. Samples were sequenced using a single index on a HiScan2000 by UD Genomed (Debrecen, Hungary) 50 bp, single end (8 samples/1 sequencing lane).…”

Section: Methodsmentioning

confidence: 99%

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Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

Baráth

Jaksa-Czotter

Molnár

et al. 2018

Viruses

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Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation.

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“…Additionally, in the analysis of the SRA samples, the percentage of the covered bases of the sequence was counted. It was previously shown that this could be used to indicate the viral presence in metagenomic samples [26,27]. A 75% genome coverage cut-off value was used for the viral presence [27].…”

Section: Occurrence Of Metmv In the Samplesmentioning

confidence: 99%

Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples

Molnár

Magyar²,

Schneider

et al. 2020

PLoS ONE

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Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.

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Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections

Cited by 18 publications

References 15 publications

Grapevine rootstocks can be a source of infection with non-regulated viruses

Grapevine rootstocks can be a source of infection with non-regulated viruses

Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples

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