Browsing by Author "De Jager, Nicholas Stratos"
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- ItemA comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria(Stellenbosch : Stellenbosch University, 2021-12) De Jager, Nicholas Stratos; Botha-Oberholster, Anna-Maria; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Institute for Plant Biotechnology.ENGLISH ABSTRACT: Diuraphis noxia (Kurdjumov, Hemiptera: Aphididae), commonly known as Russian wheat aphid (RWA), is a phloem-feeding pest capable of causing severe damage to wheat crop yields. In the United States and South Africa, rapid biotypification of this aphid has been documented, allowing it to overcome previously resistant commercial cultivars. It is speculated that differences in DNA methylation patterning allow genetically similar RWAs to become more virulent. Additionally, aphid-associated bacteria have been shown to facilitate aphid virulence in wheat (Triticum aestivum L). To establish whether these bacteria affect DNA methylation patterning in the US RWA biotypes [US1 (co-fed); US2 (co-fed); US2 (isolated)], and by extent the virulence of these biotypes, the methylation profiles and global DNA methylation and hydroxymethylation (5mC + 5hmC) levels were investigated using the methylation sensitive amplified polymorphism (MSAP) and enzyme- linked immunosorbent assay (ELISA) methods, respectively. Furthermore, whole genome bisulfite sequencing (WGBS) of these biotypes was performed and using a modified Bismark pipeline, the context of DNA methylation (CpG, CHH, CGH) was established, while differentially methylated genes (DMGs) were analysed using the Bioconductor DSS (Dispersion Shrinkage for Sequencing data) package. The results from the MSAP and ELISA methods suggested that there were differences in the DNA methylation profiles of the biotypes, suggesting indicating that aphid-associated bacteria might influence methylation in the RWA. The WGBS data revealed that generally, throughout each context and region, the less virulent biotypes [US1 (co-fed); US2 (isolated)] were more methylated (and less hemimethylated) than the more virulent biotype [US2 (co-fed)], corroborating previous findings on RWAs. More DMGs were found between the isolated and co-fed US2 populations than US1 (co-fed) and US2 (co-fed), indicating that aphid-associated bacteria had a major effect on gene methylation. Between both comparisons, several DMGs were involved in lipid metabolism and energy regulation, and some were identified to be involved in reactive oxygen species (ROS) detoxification, defence signalling during microbial invasion and sterol conversion, hinting at interactions between the aphid and its associated bacteria. Lastly, five potential effectors were predicted using a custom effector prediction pipeline.