Molecular characterization of two badnavirus genomes associated with Canna yellow mottle disease

Wijayasekara, Dulanjani; Hoyt, Peter R.; Gimondo, Austin; Dunn, Bruce L.; Thapa, Aastha; Jones, Hannah; Verchot, Jeanmarie

doi:10.1016/j.virusres.2017.10.001

Cited by 9 publications

(8 citation statements)

References 16 publications

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“…(+) indicates positive control and (-) indicates negative control. This figure is reproduced/modified from Wijayasekara et al 24 with permission. Please click here to view a larger version of this figure.…”

Section: Representative Resultsmentioning

confidence: 99%

“…This information was sufficient for prior researchers to hypothetically assign the virus to the genus Badnavirus within the family Caulimoviridae. While prior reports hypothesized that canna mottle disease in canna lilies was the result of a single badnavirus, using the metagenomics approach outlined in this study, we determined that the disease was caused by two tentative badnavirus species 24 . Thus, the strength of using a metagenome approach to discover the causal agent of a disease is that we can now identify situations where there may be more than one cause.…”

Section: Discussionmentioning

confidence: 97%

“…The contigs assembled followed by NGS were submitted into a bioinformatic workflow producing a few contigs that were identified as virus contigs. Further confirmation of two virus genomes 10,24,48,49,50 was obtained through bioinformatic analysis of RNA-seq data obtained from ribo-depleted RNA preparations. One interesting outcome was to learn that the populations of sequences recovered by DNA and RNA sequencing provided similar distributions of nonviral and viral nucleic acids.…”

Section: Discussionmentioning

confidence: 99%

“…This approach identified novel RNA and DNA virus sequences in non-cultivated plants. The steps derived from the caulimovirus isolation procedure used in this study to discover the causal agent of a disease of cultivated plants are unlike the steps derived for extracting VLP from naturally infected plants 24 . The success of both modified methods suggests that the framework procedure for caulimovirus isolation may be a valuable starting point for metagenomic studies of plant viruses in general.…”

Section: Discussionmentioning

confidence: 99%

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Verchot

Thapa

Wijayasekara

et al. 2018

JoVE

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This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components. Differential centrifugation provides further separation of virions from plant contaminants. Then proteinase K treatment removes the capsids. Then the viral DNA is concentrated and used for next-generation sequencing (NGS). The NGS data are used to assemble contigs which are submitted to NCBI-BLASTn to identify a subset of virus sequences in the generated dataset. In a parallel pipeline, RNA is isolated from infected leaves using a standard column-based RNA extraction method. Then ribosome depletion is carried out to enrich for a subset of mRNA and virus transcripts. Assembled sequences derived from RNA sequencing (RNA-seq) were submitted to NCBI-BLASTn to identify a subset of virus sequences in this dataset. In our study, we identified two related full-length badnavirus genomes in the two datasets. This method is preferred to another common approach which extracts the aggregate population of small RNA sequences to reconstitute plant virus genomic sequences. This latter metagenomic pipeline recovers virus related sequences that are retro-transcribing elements inserted into the plant genome. This is coupled to biochemical or molecular assays to further discern the actively infectious agents. The approach documented in this study, recovers sequences representative of replicating viruses that likely indicate active virus infection.

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Section: Representative Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Verchot

Thapa

Wijayasekara

et al. 2018

JoVE

Self Cite

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“…Bean yellow mosaic virus (CASTILLO et al, 1956;WYLIE et al, 2008) and Canna yellow streak virus (MONGER et al, 2007;MONGER et al, 2010;CHAUHAN et al, 2015;Alexandre et al, 2017) from the genus Potyvirus (family Potyviridae) as well as Canna yellow mottle virus (genus Badnavirus, family Caulimoviridae) (YAMASHITA et al, 1985) are the most frequent to occur. Another badnavirus, Canna yellow mottle associated virus 1, was also found on canna (WIJAYASEKARA et al, 2017). CMV (LOKHARDT, 1988) and TAV (HOLLINGS and STONE, 1971) are less common in this crop (RAJAKARUNA et al, 2014).…”

Section: Cannamentioning

confidence: 99%

Viruses infecting main ornamental plants: an overview

Митрофанова

Zakubanskiy

Митрофанова

2018

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Ornamental plants are cultivated for decorative and utility purposes in urban landscapes throughout the world. They are much valued for their aesthetic properties and constitute an important part of the global horticulture industry. Plant viruses and viroids of various taxonomic groups have a significant negative impact on ornamentals provoking a wide range of symptoms, reducing both decorative value and quality of propagated material and causing large economic damage. A significant growth of the ornamental plants market in recent years promotes the spread of viral diseases. Therefore, systematization of data on virus and viroid phytopathogens diversity in these cultures is an urgent research task. Among the most popular ornamentals are chrysanthemum, rose, clematis, canna, and lavender. More than fifty viruses and viroids from 17 different families (including two viroid families) have been identified in these crops to date. In the presented review, we described the variety of these pathogens and their effect on the above-mentioned ornamentals.

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