Doctoral Degrees (Genetics)
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Browsing Doctoral Degrees (Genetics) by Subject "Apples -- Diseases and pests"
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- ItemSmall RNA profiling of virus-infected apple plants(Stellenbosch : Stellenbosch University, 2014-12) Visser, Marike; Burger, Johan T.; Maree, H. J.; Rees, Jasper; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.ENGLISH ABSTRACT: Apple stem grooving virus (ASGV) is globally associated with latent infection in commercial apple trees. Little is known about this plant-‐virus interaction. This study made use of next-‐generation sequencing to investigate the effect of virus-‐infection on the expression of the different small RNA (sRNA) species namely, miRNAs, nat-‐siRNAs, phasiRNAs, rasiRNAs, tRNA-‐derived sRNAs and vsiRNAs. Broad and narrow size-‐range datasets were generated using sRNA libraries prepared from total and size-‐selected RNA, respectively. Through bioinformatic data analyses, 130 genomic loci were predicted to give rise to miRNAs, 85 of which were novel MIR genes. Targets were predicted for the majority of miRNAs, a few of which could be validated with a publicly available degradome dataset. Cis-‐ and trans-‐natural antisense transcripts (NATs) were identified, of which only the latter were highly enriched for sRNAs in their overlapping regions. Transcript as well as genomic regions were also identified that can give rise to phasiRNAs. For 25 of these loci an in-‐phase miRNA target site was identified, half of which could be validated with the degradome dataset. Nearly all apple repeat sequences in Repbase were associated with sRNA synthesis. sRNAs derived from both ends of mature tRNAs were identified. These sRNAs corresponded to tRFs and tRNA-‐halves. Reads associated with tRNA-‐halves were prominent in the broad range datasets. sRNAs, originating from the central regions of tRNAs, were also observed. Analysis of the vsiRNAs suggested the presence of two ASGV genetic variants in two of the samples, while the third sample was infected with only one variant. Comparison of the vsiRNA profiles generated from the two datasets highlighted the influence of library preparation on the interpretation of results. Differential expression analysis of the identified apple sRNA species showed no variation between healthy and infected plants, except for the tRNA-‐derived sRNAs, which did show altered expression levels. Taken together, the various sRNA species characterised in this study significantly extended the existing knowledge of apple sRNAs and provide a broad platform for future functional studies in apple. This study also presents the first and most comprehensive report on sRNAs involved in ASGV infection in apple.