Identification and characterization of a viroid resembling apple dimple fruit viroid in fig (Ficus carica L.) by next generation sequencing of small RNAs

Chiumenti, Michela; Torchetti, Enza Maria; Serio, Francesco Di; Minafra, A.

doi:10.1016/j.virusres.2014.03.026

Cited by 43 publications

(24 citation statements)

References 39 publications

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“…All rod-shaped viroids, independently of GC contents, group with 23S (D1) and 16S (D2) rRNAs, indicating ancient origins . a Citrus viroid IV (Puchta et al, 1991 ); b Tomato planta macho viroid, tomato apical stunt viroid (Kiefer et al, 1983 ); c Avocado sunblotch viroid, Potato spindle tuper viroid, Chrysanthemum stunt viroid (Symons, 1981 ); d Pear blister canker viroid (Hernandez et al, 1992 ); e Apple dimple fruit viroid, (Chiumenti et al, 2014 ); f Citrus exocortis viroid, Hop stunt viroid (Lin et al, 2015 ) . …”

Section: Resultsmentioning

confidence: 99%

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

Seligmann

Raoult

2018

Front. Microbiol.

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We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5′ UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing).

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Section: Resultsmentioning

confidence: 99%

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

Seligmann

Raoult

2018

Front. Microbiol.

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“…More recently developed methods, such as reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN), micro-and macroarrays and next-generation sequencing (NGS), enable even faster and more sensitive detection of viroid infections (Hadidi et al, 2004;Boubourakas et al, 2009;Owens et al, 2012;Chiumenti et al, 2014). Methods that have been used in viroid diagnostics are representatively summarized in Table 1.…”

Section: Methods For Viroid Detectionmentioning

confidence: 99%

“…NGS is being increasingly used in plant virology, due to quick identification either from total RNA or indirect detection by analysing short interfering RNAs (siRNA) . NGS of siRNAs provides detection of viroids that occur as latent infections, at an extremely low concentration, or are even unknown (Barba et al, 2014;Chiumenti et al, 2014). Sequences of the total small RNAs of infected plants obtained by deep sequencing can be analysed using a computational algorithm for the homology-independent discovery of replicating circular RNAs, called PFOR (progressive filtering of overlapping small RNAs) (Wu et al, 2012).…”

Section: Rt-qpcrmentioning

confidence: 99%

“…Among the most researched are grapevine viroids, which have been detected by NGS mainly as part of more significant virus infection (Al Rwahnih et al, 2009;Giampetruzzi et al, 2012;Poojari et al, 2013). NGS technologies can also be applied for the identification of viroids that are not expected to be pathogens of certain hosts, as has been the case with apple dimple fruit viroid (ADFVd) in fig (Ficus carica) (Chiumenti et al, 2014) and CBCVd in hop (Humulus lupulus) (Jakse et al, 2015).…”

Section: Rt-qpcrmentioning

confidence: 99%

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Diagnostic techniques for viroids

et al. 2016

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The fast growth of the human population forces us to produce more food, but higher crop production also leads to the fast spread of diseases. Plant pathology deploys a wide range of methods that do not provide an adequate solution to all disease losses. In the case of viroids, therapeutic means of control are not available; therefore control strategies are more focused on the development of reliable detection methods to quickly exclude the infected plant material. Although viroids are the smallest and simplest plant pathogens, their identification and detection is not straightforward. Each viroid–host combination is specific, and for reliable identification, all steps from sampling to final detection must be performed accurately. In this review, several methods for viroid detection in various host plants are discussed, including their advantages and disadvantages. Even though relatively new molecular methods enable fast and sensitive detection of viroids, a combination of different methods gives the most reliable identification. Techniques based on nucleic acids may be the future for viroid detection but they still cannot replace biological indexing, which is usually essential in epidemiological and aetiological studies.

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“…Therefore, besides being molecular markers of ongoing viroid infections, overlapping vd-sRNAs can be assembled in silico into viroid contigs to subsequently search for similar sequences in databanks (as previously shown for plant viruses). Several viroids have been detected by this approach in the last few years [1,5,26,36,48,68]. In 2012, an algorithm was developed to assemble circular RNA genomes from small RNAs resulting from NGS, thus allowing identification of viroid-like RNAs independent of any homology with previously reported sequences [67].…”

Section: Validity Of Recognized Species Of Genus Pospiviroidmentioning

confidence: 99%

Current status of viroid taxonomy

Serio

Flores

Verhoeven³

et al. 2014

Arch Virol

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157

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Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of nextgeneration sequencing and bioinformatics for known and previously unrecognized viroids.

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Identification and characterization of a viroid resembling apple dimple fruit viroid in fig (Ficus carica L.) by next generation sequencing of small RNAs

Cited by 43 publications

References 39 publications

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA

Diagnostic techniques for viroids

Current status of viroid taxonomy

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