In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection

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dc.contributor.authorVisser, Marikeen_ZA
dc.contributor.authorCook, Glynnisen_ZA
dc.contributor.authorBurger, Johan T.en_ZA
dc.contributor.authorMaree, Hans J.en_ZA
dc.date.accessioned2017-10-25T10:19:22Z
dc.date.available2017-10-25T10:19:22Z
dc.date.issued2017
dc.descriptionCITATION: Visser, M., et al. 2017. In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection. Virology Journal, 14:200, doi:10.1186/s12985-017-0871-9.en_ZA
dc.descriptionThe original publication is available at https://virologyj.biomedcentral.comen_ZA
dc.descriptionPublication of this article was funded by the Stellenbosch University Open Access Fund.en_ZA
dc.description.abstractBackground: Small RNA (sRNA) associated gene regulation has been shown to play a significant role during plant-pathogen interaction. In commercial citrus orchards co-infection of Citrus tristeza virus (CTV) and viroids occur naturally. Methods: A next-generation sequencing-based approach was used to study the sRNA and transcriptional response in grapefruit to the co-infection of CTV and Citrus dwarfing viroid. Results: The co-infection resulted in a difference in the expression of a number of sRNA species when comparing healthy and infected plants; the majority of these were derived from transcripts processed in a phased manner. Several RNA transcripts were also differentially expressed, including transcripts derived from two genes, predicted to be under the regulation of sRNAs. These genes are involved in plant hormone systems; one in the abscisic acid, and the other in the cytokinin regulatory pathway. Additional analysis of virus- and viroid-derived small-interfering RNAs (siRNAs) showed areas on the pathogen genomes associated with increased siRNA synthesis. Most interestingly, the starting position of the p23 silencing suppressor’s sub-genomic RNA generated a siRNA hotspot on the CTV genome. Conclusions: This study showed the involvement of various genes, as well as endogenous and exogenous RNA-derived sRNA species in the plant-defence response. The results highlighted the role of sRNA-directed plant hormone regulation during biotic stress, as well as a counter-response of plants to virus suppressors of RNA-silencing.en_ZA
dc.description.urihttps://virologyj.biomedcentral.com/articles/10.1186/s12985-017-0871-9
dc.description.versionPublisher's versionen_ZA
dc.format.extent10 pages : illustrationsen_ZA
dc.identifier.citationVisser, M., et al. 2017. In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection. Virology Journal, 14:200, doi:10.1186/s12985-017-0871-9en_ZA
dc.identifier.issn1743-422X (online)
dc.identifier.otherdoi:10.1186/s12985-017-0871-9
dc.identifier.urihttp://hdl.handle.net/10019.1/102383
dc.language.isoen_ZAen_ZA
dc.publisherBioMed Centralen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectBiotic stressen_ZA
dc.subjectCitrus paradisien_ZA
dc.subjectGrapefruit sRNAen_ZA
dc.subjectRNA viruses -- Genetic aspectsen_ZA
dc.subjectCitrus tristeza virus (CTV)en_ZA
dc.subjectPlant-pathogen interactionen_ZA
dc.titleIn silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infectionen_ZA
dc.typeArticleen_ZA
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