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

Abstract

BackgroundSmall 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.MethodsA 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.ResultsThe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (10.1186/s12985-017-0871-9) contains supplementary material, which is available to authorized users.

Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

“…Pursuing the former objective, Zablocki & Pietersen [ 92 ] and Read & Pietersen [ 93 ] provided evidence through HTS analysis regarding the isolates associated with the breaking of CTV cross-protection in grapefruit industry, characterizing recombination events, and fine population mapping, even at a single gene level. An example of the study of fine molecular virus–host interactions is the report of Visser et al [ 94 ] who sequenced siRNAs and transcripts on grapefruit co-infected by CTV and Citrus dwarfing viroid . Analyzed siRNAs showed the pathogen regions associated with increased silencing and an altered plant hormone regulatory pattern.…”

Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock

“…Furthermore, HTS allows the discovery of rare transcripts, which would be difficult to identify using traditional methods such as microarrays, and is more time efficient than an RT-qPCR approach. More specifically, in citrus, HTS analysis of mRNA has been widely used to understand host responses to pathogens such as 'Candidatus' Liberibacter asiaticus [27][28][29][30] and citrus tristeza virus [28,31].…”