The complete nucleotide sequence and genomic characterization of grapevine asteroid mosaic associated virus

Vargas-Asencio, José; Wojciechowska, Klaudia; Baskerville, Maia; Gomez, Annika L.; Perry, Keith L.; Thompson, Jeremy R.

doi:10.1016/j.virusres.2016.10.001

Cited by 16 publications

(6 citation statements)

References 32 publications

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“…From medicine, clinical diagnostic, microbiology to ecology, plant pathology (and more specifically plant virology) seems to have benefited the most from these new tools. Grapevine research also improved with HTS, with many new viruses being identified all over the world, belonging to different families such as Betaflexiviridae (Al Rwahnih et al, 2012; Giampetruzzi et al, 2012; Jo et al, 2017a,b; Blouin et al, 2018a,b; Candresse et al, 2018; Diaz-Lara et al, 2018), Caulimoviridae (Zhang et al, 2011), Luteoviridae (Silva et al, 2017), Secoviridae (Al Rwahnih et al, 2016), or Tymoviridae (Al Rwahnih et al, 2009; Beuve et al, 2015; Cretazzo and Velasco, 2017; Vargas-Asencio et al, 2017). HTS technologies have been confirmed to be a powerful diagnostic tool allowing for an exhaustive description of viral species present in many grapevine sample (Coetzee et al, 2010; Al Rwahnih et al, 2011; Jo et al, 2015; Beuve et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

et al. 2018

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In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more “reductionist” view focusing on one or a few known agents, HTS-based approaches are able to give a “holistic snapshot” of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.

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Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

et al. 2018

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“…Each resulting RNA preparation was divided into two aliquots to be used as input for sRNA-Seq and degradome libraries. sRNA libraries were prepared from 1 mg of total RNA using methods described previously (Vargas-Asencio et al, 2017). For the degradome libraries,~40 mg of total RNA was used.…”

Section: Plant Growth Conditions Rna Extraction and Library Preparamentioning

confidence: 99%

A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs

Vargas-Asencio

Perry

2020

Front. Plant Sci.

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Gene regulation involves the orchestrated action of multiple regulators to fine-tune the expression of genes. Hierarchical interactions and co-regulation among regulators are commonly observed in biological systems, leading to complex regulatory networks. Small RNA (sRNAs) have been shown to be important regulators of gene expression due to their involvement in multiple cellular processes. In plants, microRNA (miRNAs) and phased small interfering RNAs (phasiRNAs) correspond to two well-characterized types of sRNAs involved in the regulation of posttranscriptional gene expression, although information about their targets and interactions with other gene expression regulators is limited. We describe an extended sRNA-mediated regulatory network in Arabidopsis thaliana that provides a reference frame to understand sRNA biogenesis and activity at the genomewide level. This regulatory network combines a comprehensive evaluation of phasiRNA production and sRNA targets supported by degradome data. The network includes 17% of genes in the A. thaliana genome, representing~50% annotated gene ontology (GO) functional categories. Approximately 14% of genes with GO annotations corresponding to regulation of gene expression were found to be under sRNA control. The unbiased bioinformatic approach used to produce the network was able to detect 107 PHAS loci (regions of phasiRNA production), 5,047 active phasiRNAs (~70% of which were non-canonical), and reconstruct 17 regulatory modules resulting from complex regulatory interactions between different sRNA-regulatory pathways. Known regulatory modules like miR173-TAS-PPR/TPR and miR390-TAS3-ARF/F-box were faithfully reconstructed and expanded, illustrating the accuracy and sensitivity of the methods and providing confidence for the validity of findings of previously unrecognized modules. The network presented here includes a 2X increase in the number of identified PHAS loci, a large complement (~70%) of non-canonical phasiRNAs, and the most comprehensive

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“…Another technique which does not rely on prior sequence knowledge is mass spectrometry which, in contrast to other methods, can derive sequences from protein. This technique is under-utilised [ 28 , 29 , 30 ] in plant virus detection and characterisation. Below, future and existing activities to upgrade our national border diagnostics capacity and capabilities by harnessing the benefits of new technologies are discussed.…”

Section: New and Old Technologiesmentioning

confidence: 99%

New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand

Delmiglio

Waite

Lilly

et al. 2023

Viruses

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To protect New Zealand’s unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies.

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The complete nucleotide sequence and genomic characterization of grapevine asteroid mosaic associated virus

Cited by 16 publications

References 32 publications

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs

New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand

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