Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya

Melcher, Ulrich; Muthukumar, Vijay; Wiley, Graham B.; Min, Byoung Eun; Palmer, Michael W.; Verchot, Jeanmarie; Ali, Akhtar; Nelson, Richard S.; Roe, Bruce A.; Thapa, Vaskar; Pierce, Margaret L.

doi:10.1016/j.jviromet.2008.05.030

Cited by 47 publications

(26 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The present study also confirms that both VANA [13] and siRNA [16] can be successfully targeted by metagenomics approaches for the discovery and characterization of plant-infecting DNA viruses. The VANA-based 454 pyrosequencing approach has several advantages as it initially combines reverse-transcriptase priming and a Klenow Fragment step, which potentially enables the detection of both RNA and DNA viruses.…”

Section: Discussionsupporting

confidence: 80%

“…Three main classes of nucleic-acids have been targeted by such analyses: (1) virion-associated nucleic acids (VANA) purified from viral particles [13], [14]; (2) double-stranded RNAs (dsRNA) [15]; and (3) virus-derived small interfering RNAs (siRNAs) [16]. Large numbers of both known and new plant and fungus infecting DNA and RNA viruses and viroids have been detected using these approaches [12], [17]–[21].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

et al. 2014

View full text Add to dashboard Cite

Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.

show abstract

Section: Discussionsupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

et al. 2014

View full text Add to dashboard Cite

show abstract

“…This virus specifically was identified as a badnavirus which belongs to the Caulimoviridae family [38]. Caulimoviridae are known to be plant pararetroviruses that replicate their genome through a process of reverse transcription [39].…”

Section: Discussionmentioning

confidence: 99%

Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species

et al. 2013

View full text Add to dashboard Cite

Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.

show abstract

“…Another approach to simplifying sequence datasets is the use of bioinformatic or molecular approaches in pre-sequencing or post-sequencing steps that enrich for pathogen- or microbe-related sequences (Melcher et al, 2008). For example, multiple researchers have utilized the pool of small RNAs (sometimes called the degradome) as a target pool of nucleic acids that are enriched for viral sequences via plant defense responses (Donaire et al, 2009; Kreuze et al, 2009; Pantaleo et al, 2010; Kashif et al, 2012; Li et al, 2012; Loconsole et al, 2012; Roy et al, 2013a,b).…”

Section: Taxonomic Classification Of Ngs Reads: Approachesmentioning

confidence: 99%

Metagenomic search strategies for interactions among plants and multiple microbes

2014

Self Cite

View full text Add to dashboard Cite

Plants harbor multiple microbes. Metagenomics can facilitate understanding of the significance, for the plant, of the microbes, and of the interactions among them. However, current approaches to metagenomic analysis of plants are computationally time consuming. Efforts to speed the discovery process include improvement of computational speed, condensing the sequencing reads into smaller datasets before BLAST searches, simplifying the target database of BLAST searches, and flipping the roles of metagenomic and reference datasets. The latter is exemplified by the e-probe diagnostic nucleic acid analysis approach originally devised for improving analysis during plant quarantine.

show abstract

Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya

Cited by 47 publications

References 25 publications

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

Appearances Can Be Deceptive: Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context

Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species

Metagenomic search strategies for interactions among plants and multiple microbes

Contact Info

Product

Resources

About