Extant hybrids of RNA viruses and viroid-like elements

Forgia, Marco; Navarro, Beatriz; Daghino, Stefania; Cervera, Amelia; Gisel, Andreas; Perotto, Silvia; Aghayeva, Dilzara N.; Akinyuwa, Mary Funmilayo; Gobbi, Emanuela; Zheludev, I.N.; Edgar, Robert C.; Chikhi, Rayan; Turina, Massimo; Babaian, Artem; Serio, Francesco Di; Peña, Marcos de la

doi:10.1101/2022.08.21.504695

Cited by 6 publications

(3 citation statements)

References 38 publications

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“…Viroid and more generally circular non-coding RNA research is a productive field with an increasing number of reports the last few years (Cervera and de la Peña, 2020;Forgia et al, 2023). Understanding the mechanisms involved in viroid biological cycle will pave the way to elucidate how these interesting pathogens despite their simplicity manage to be so successful in nature.…”

Section: Discussionmentioning

confidence: 99%

PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

Tselika,

Belmezos,

Kallemi

et al. 2023

Front. Plant Sci.

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Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.

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Section: Discussionmentioning

confidence: 99%

PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

Tselika,

Belmezos,

Kallemi

et al. 2023

Front. Plant Sci.

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“…A small proportion of viruses lack capsids, and here, the appropriate Baltimore group is determined by phylogenetic relatedness to viruses with capsids. Depending on species, RNA viruses can have segmented or nonsegmented genomes that are almost always linear, but in a few cases (notably chuviruses and the recently discovered ambiviruses) are or appear to be circular ( Li et al 2015 ; Forgia, Navarro, et al 2022 ; Lee et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Olendraitė

Brown

Firth

2023

Molecular Biology and Evolution

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RNA viruses are abundant, highly diverse, and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost effectively expand the diversity of known RNA virus sequences we mined publicly available transcriptomic datasets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA dependent RNA polymerase – the only universal “hall-mark” gene of RNA viruses. By using these to search the NCBI Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analysed their diversity, taxonomic classification, phylogeny and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp pHMMs provide a useful resource for the virus discovery community.

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“…A small proportion of viruses lack capsids, and here the appropriate Baltimore group is determined by phylogenetic relatedness to viruses with capsids. Depending on species, RNA viruses can have segmented or non-segmented genomes that are almost always linear, but in a few cases (notably chuviruses and the recently discovered ambiviruses) are or appear to be circular (Li et al, 2015; Forgia et al, 2022b; Lee et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Identification of RNA virus-derived RdRp sequences in publicly available transcriptomic datasets

Olendraitė

Brown

Firth

2022

Preprint

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RNA viruses are abundant, highly diverse, and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost effectively expand the diversity of known RNA virus sequences we mined publicly available transcriptomic datasets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA dependent RNA polymerase - the only universal "hall-mark" gene of RNA viruses. By using these to search the NCBI Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analysed their diversity, taxonomic classification, phylogeny and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp pHMMs provide a useful resource for the virus discovery community.

show abstract

Extant hybrids of RNA viruses and viroid-like elements

Cited by 6 publications

References 38 publications

PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

Identification of RNA virus-derived RdRp sequences in publicly available transcriptomic datasets

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