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Rolling circle replication (RCR) in the Pospiviroidae and the Avsunviroidae. The members of Pospiviroidae replicate by the asymmetric RCR mechanism (A) inside the host nucleus with the help of the host enzymes. The circular + strand (Red) of viroid RNA is copied into the-strand (Blue) by the RCR, which is linearized by the host RNases, and the linear RNA is then used as the template for the synthesis of the + strand. Finally, the host ligases circularize the viroid RNAs. As shown in panel (B), the members of Avsunviroidae replicate by the symmetric rolling circle mechanism using the nuclear-encoded polymerase (NEP) in the chloroplast. Replication of RNA strands with both polarities are completed by the RCR mechanism. In this family, the viroid RNAs have autocatalytic ribozymes that catalyze the cleavage of the circular oligomeric form of the viroid RNAs into monomers (Diagram adapted from the Flores et al. FEBS Letters 567, 2004).
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Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex...
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... brief overview is given in Table 1 (see Supplementary Data, Table S1 for detailed elaboration) [16]. Both families of viroids adopt the rolling-circle replication (RCR) mechanism, but the Pospiviridae replicate by asymmetric and the Avsunviridae by symmetric rolling-circle mechanisms (Figure 2). Pospiviroidae replicates in the nucleus, where the host DNA dependent RNA polymerase II is involved in the transcription of the viroid RNA [17]. ...
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... Recent reports have shown a relation between RNA silencing and viroid replication. Viroids are free RNA molecules which do not code for any protein and are similar to circular lncR-NAs [172]. Several horticulture crops such as the apple, avocado, grapevine, peach, tomato, etc., are facing viroid infections. ...
Viruses are silent enemies that intrude and take control of the plant cell's machinery for their own multiplication. Infection by viruses and the resulting damage is still a major challenge in the agriculture sector. Plants have the capability to fight back, but the ability of viruses to mutate at a fast rate helps them to evade the host's response. Therefore, classical approaches for introgressing resistance genes by breeding have obtained limited success in counteracting the virus menace. Genetic modification (GM)-based strategies have been successful in engineering artificial resistance in plants. Several different approaches based on pathogen-derived resistance, antisense constructs, hairpin RNAs, double-stranded RNA, etc., have been used to enhance plants' resistance to viruses. Recently, genome editing (GE) strategies mainly involving the CRISPR/Cas-mediated modifications are being used for virus control. In this review, we discuss the developments and advancements in GM-and GE-based methods for tackling viral infection in plants.
... Intriguingly, many defective/defective interfering (D/DI) RNAs, satellite RNAs, and even incompletely degraded viral genomic RNAs are considered to be lncRNAs [191][192][193][194] (Fig 3A). They have the non-protein-coding features and are involved in the host-virus interactions. ...
... For example, citrus tristeza virus (CTV) produces a lncRNA called low molecular weight tristeza 1 (LMT1), which is involved in maintaining the accumulation, movement, and infectivity of the virus by lowering the production of SA and reactive ROS required for antiviral defense [195]. CMV Y-and Q-satRNAs, which are 300 to 400 nt in size and do not encode any functional protein, probably function as lncRNAs [192]. CMV Y-satRNA functions as an siRNA addition, the lncRNAs ANX2 and RLP7 in cotton decrease the expression of their neighboring genes, regulate the JA response by affecting the JA pathway genes, LOX1 and LOX, and promote the infection of V. dahliae and B. cinerea. ...
... precursor to produce Y-sat siRNAs and targets the host ChlI mRNA to bring in bright yellowing symptoms in tobacco, while CMV Q-satRNA can bind to a bromodomain-containing protein (BRP) and probably plays a role in histone remodeling [192,196]. However, the virulence of CMV Y-satRNA results from sRNAs derived from satRNAs, and the role of CMV Q-satRNA has not been verified, which makes it controversial to group these satRNAs as lncRNAs [197,198]. ...
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... Among these were 23 maize miRNAs that were responsible for regulating plant development and metabolism (Ghorbani et al., 2018). Moreover, cucumber green mottle mosaic virus infection of watermelon results in differential expression of 548 and 67 lncRNAs, which are responsible for phenylalanine metabolism, citrate cycle, and endocytosis (Shrestha & Józef, 2020;Sun et al., 2020). Taken together, all the above results demonstrate the complex nature of lncRNAs and cir-cRNAs in defence signalling pathways and indicate their function in the regulation of defence response genes. ...
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... Conceivably, the transmitted cellular sequences; possibly along with transmitted bacteria-derived sequences; could become autonomous replicating elements. Indeed, the isolated non-coding cellular sequences could take the form of viroid's as occur in plants [38][39][40]. This does not apply to the prototype SCMV-derived stealth adapted virus since there are still genetic sequences corresponding to approximately half of originating SCMV genome in the more than 200 clones on which sequence data have been obtained. ...
... Indeed, the isolated non-coding cellular sequences could take the form of viroids as occur in plants. [38][39][40] This does not apply to the prototype SCMV-derived stealth adapted virus since there are still genetic sequences corresponding to approximately half of originating SCMV genome in the more than 200 clones on which sequence data have been obtained. Interestingly, there is a very uneven distribution of the matching clones with some regions predominantly represented. ...
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... A particular interesting type of DVG is known as defective interfering particles (DIPs), which show the capacity to encapsulate and interfere with the replication and population dynamics of the wild-type virus [6]. In a recent review, DVGs have been considered as long noncoding RNAs, though they might preserve some coding capacity [7]. In the case of negative-sense RNA virus, the terminology has to be reverted accordingly: coding (+) by non-coding (−), 5 cb/sb by 3 cb/sb, and "forward" by "reverse" and vice versa. ...
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program also generates output files in user-friendly HTML format, which can help users to explore the DVGs identified in the sample. We evaluated the performance of DVGfinder compared to the two search algorithms used separately and found that it slightly improves sensitivities for low-coverage synthetic HTS data and DI-tector precision for high-coverage samples. The metasearch program also showed higher sensitivity on a real sample for which a set of copy-backs were previously validated.
... It is true that there are several previous studies that have detected sgRNA2-like molecules from viruses belonging to the genus Potexvirus (26,27), and the possibility that these viral RNAs have some function cannot be completely ruled out. Some of the degradation intermediates of viral RNAs accumulate in large amounts and function as noncoding RNAs (28), and sgRNA2-like molecules may also accumulate under certain conditions and have some function. However, the present results indicate that sgRNA1, not sgRNA2, is responsible for the conserved function as the major template of the translation of TGBp2 and TGBp3. ...
Potexvirus , a group of plant viruses, infect a variety of crops, including cultivated crops. It has been thought that the three transition proteins that are essential for the cell-to-cell transfer of potexviruses are translated from two subgenomic RNAs, sgRNA1 and sgRNA2.
... A particular interesting type of DVG is known as defective interfering particles (DIPs), which show the capacity to encapsulate and interfere with the replication and population dynamics of the wild-type virus [5]. In a recent review, DVGs have been considered as long noncoding RNAs, though they might preserve some coding capacity [6]. ...
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing data has become an interesting computational problem. Up to nowadays, several algorithms have been proposed, though all incur in false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. Here we develop a novel software, DVGfinder, that wraps the two most commonly used algorithms into a pipeline that predicts DVGs. Using a gradient boosting classifier machine learning algorithm, we evaluate the performance of DVGfinder compared to previous algorithms and found that it outcompetes their precision and sensitivity in simulated datasets. DVGfinder generates user-friendly output files in HTML format that can assist users to identify DVGs based on their associated probability of being true positives.
... Viroids are single-stranded circular non-coding RNAs that are the smallest infectious entities (between 246 and 401 nt in length) of plants and do not encode any protein. Viroids can replicate individually in the host plant nucleus or chloroplast by using host RNA polymerases through asymmetric and symmetric rolling-circle mechanisms [64]. Although many viroids were initially identified by their symptoms on infected plants, it is now known that viroids can also infect hosts asymptomatically [65]. ...
... Virusoids replicate through a rollingcircle mechanism based on RNA intermediates and are dependent on helper viruses or host plants. In contrast to viroids, virusoids are encapsidated by the helper virus coat protein [64,71]. The similarities between viroids and virusoids have led to the hypothesis that these circular RNAs may have a monophyletic origin [71]. ...
Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications. View Full-Text
Keywords: grapevine; viral disease; diagnostic methods; RNA sequencing; nanopore sequencing technology; RNA modifications
... Viroids are single-stranded circular non-coding RNAs that are the smallest infectious entities (between 246 and 401 nt in length) of plants and do not encode any protein. Viroids can replicate individually in the host plant nucleus or chloroplast by using host RNA polymerases through asymmetric and symmetric rolling-circle mechanisms [64]. Although many viroids were initially identified by their symptoms on infected plants, it is now known that viroids can also infect hosts asymptomatically [65]. ...
... Virusoids replicate through a rollingcircle mechanism based on RNA intermediates and are dependent on helper viruses or host plants. In contrast to viroids, virusoids are encapsidated by the helper virus coat protein [64,71]. The similarities between viroids and virusoids have led to the hypothesis that these circular RNAs may have a monophyletic origin [71]. ...
Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses and their diagnostic methods, the principle of nanopore sequencing technology and its application in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications.
