Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

Kreuze, Jan; Pérez, Antonio Martín; Untiveros, Milton; Quispe, Dora; Fuentes, Segundo; Barker, Ian K.; Simon, Reinhard

doi:10.1016/j.virol.2009.03.024

Cited by 534 publications

(424 citation statements)

References 22 publications

Supporting

Mentioning

411

Contrasting

Unclassified

Order By: Relevance

“…Hence, small RNA-based diagnostics of viruses benefit from the accumulation of sequence data of novel (Schoebel et al, 2014). Compared with mRNA sequencing, small RNA deep sequencing enriches the sequence pool for viral sequences and the advantage of this method over high-throughput sequencing of dsRNA is that small RNA deep sequencing may allow detection of a wider variety of viruses, including those with ssRNA or DNA genomes (Kreuze et al, 2009;Kashif et al, 2012). The novel putative mitovirus detected in this study has an ssRNA genome and remained undetected using a conventional cloning approach (Kashif et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

Vainio¹,

Jurvansuu²,

Streng

et al. 2015

Journal of General Virology

View full text Add to dashboard Cite

Analysis of virus-derived small RNAs with high-throughput sequencing has been successful for detecting novel viruses in plants and invertebrates. However, the applicability of this method has not been demonstrated in fungi, although fungi were among the first organisms reported to utilize RNA silencing. Here, we used virus-infected isolates of the fungal species complex Heterobasidion annosum sensu lato as a model system to test whether mycovirus genome segments can be detected with small RNA deep sequencing. Species of the genus Heterobasidion are some of the most devastating forest pathogens in boreal forests. These fungi cause wood decay and are commonly infected with species of the family Partitiviridae and the unassigned virus species Heterobasidion RNA virus 6. Small RNA deep sequencing allowed the simultaneous detection of all eight double-stranded RNA virus strains known to be present in the tested samples and one putative mitovirus species (family Narnaviridae) with a single-stranded RNA genome, designated here as Heterobasidion mitovirus 1. Prior to this study, no members of the family Narnaviridae had been described as infecting species of Heterobasidion. Quantification of viral double-and single-stranded RNA with quantitative PCR indicated that co-infecting viral species and viruses with segmented genomes can be detected with small RNA deep sequencing despite vast differences in the amount of RNA. This is the first study demonstrating the usefulness of this method for detecting fungal viruses. Moreover, the results suggest that viral genomes are processed into small RNAs by different species of Heterobasidion.

show abstract

Section: Discussionmentioning

confidence: 99%

“…Consequently, the analysis of virus-derived small RNAs with high-throughput sequencing has been successfully used in plants and invertebrates to detect novel viruses (Kreuze et al, 2009;Pantaleo et al, 2010;Wu et al, 2010;Bi et al, 2012;Kashif et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

Vainio¹,

Jurvansuu²,

Streng

et al. 2015

Journal of General Virology

View full text Add to dashboard Cite

show abstract

“…Moreover, CTV sRN As ad opt an asym m etric d istribution along the viral gRN A, w ith a m ajor hotspot covering approxim ately the 3'-term inal 2500 nt. Such a pronounced uneven d istribution has not been reported in other RN A viruses, includ ing one m em ber of the sam e fam ily (Kreuze et al 2009). …”

mentioning

confidence: 82%

Citrus tristeza virus infection induces the accumulation of viral small RNAs (21–24-nt) mapping preferentially at the 3′-terminal region of the genomic RNA and affects the host small RNA profile

et al. 2011

View full text Add to dashboard Cite

“…NGS of small RNA libraries of plants resulted in a wealth of de novo virus genome assembly, and the method demonstrated to be powerful both for detection of known viruses, and new virus genome assembly ( Kreuze et al, 2009 andVainio et al, 2015). A summary of the main features of each of the sequenced libraries is displayed in Table 1 together with the SRA accession number for each library.…”

Section: Assembly Of Mycovirus Sequences From Srna Librariesmentioning

confidence: 99%

“…This idea comes from the work of Kreuze et al 2009 where the authors showed the possibility to assemble new and unknown viral sequences from sRNA libraries obtained from plants. To our knowledge, such an approach has only very recently been used for de novo assembly of viral genomes from fungi ( Vainio et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Nerva¹,

et al. 2016

View full text Add to dashboard Cite

Highlights• First report of mycoviruses isolated from fungi from marine environment.• Survey of mycoviruses using multiple approaches for both DNA and RNA genomes.• RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses.• Twelve new virus species were characterized molecularly.• Expression of a viral RNA from an endogenized cDNA segment. AbstractThe number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment.

show abstract

Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

Cited by 534 publications

References 22 publications

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs

Citrus tristeza virus infection induces the accumulation of viral small RNAs (21–24-nt) mapping preferentially at the 3′-terminal region of the genomic RNA and affects the host small RNA profile

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

Contact Info

Product

Resources

About