Small RNA profiling of virus-infected apple plants

[摘要] ENGLISH ABSTRACT: Apple stem grooving virus (ASGV) is globally associated with latent infection in commercial apple trees.Littleis known about this plant-­‐virus interaction.This study made use ofnext-­‐generation sequencing to investigate the effect of virus-­‐infection on the expression of the different small RNA (sRNA) speciesnamely, miRNAs, nat-­‐siRNAs, phasiRNAs, rasiRNAs, tRNA-­‐derivedsRNAs and vsiRNAs.Broad and narrow size-­‐range datasets were generated using sRNA libraries prepared from total and size-­‐selectedRNA, respectively.Through bioinformatic data analyses, 130 genomicloci were predicted to give rise to miRNAs, 85 of which were novelMIR genes.Targets were predicted for the majority of miRNAs, afew of which could be validated with a publicly available degradomedataset.Cis-­‐ and trans-­‐natural antisense transcripts (NATs) wereidentified, of which only the latter were highly enriched for sRNAsin their overlapping regions.Transcript as well as genomic regionswere also identified that can give rise to phasiRNAs.For 25 of theseloci an in-­‐phase miRNA target site was identified, half of which couldbe validated with the degradome dataset.Nearly all apple repeat sequences in Repbase were associated with sRNA synthesis.sRNAsderived from both ends of mature tRNAs were identified.ThesesRNAs corresponded to tRFs and tRNA-­‐halves.Reads associatedwith tRNA-­‐halves were prominent in the broad range datasets.sRNAs, originating from the central regions of tRNAs, were alsoobserved.Analysis of the vsiRNAs suggested the presence of twoASGV genetic variants in two of the samples, while the third samplewas infected with only one variant.Comparison of the vsiRNA profilesgenerated from the two datasets highlighted the influence of librarypreparation on the interpretation of results.Differential expressionanalysis of the identified apple sRNA species showed no variationbetween healthy and infected plants, except for the tRNA-­‐derivedsRNAs, which did show altered expression levels.Taken together,the various sRNA species characterised in this study significantlyextended the existing knowledge of apple sRNAs and provide abroad platform for future functional studies in apple.This studyalso presents the first and most comprehensive report on sRNAsinvolved in ASGV infection in apple.

[发布机构] Stellenbosch University