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A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria
Thesis (MScAgric)--Stellenbosch University, 2021.
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Stellenbosch : Stellenbosch University
2021
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| _version_ | 1867614138281230336 |
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| access_status_str | Open Access |
| author | De Jager, Nicholas Stratos |
| author2 | Botha-Oberholster, Anna-Maria |
| author_browse | Botha-Oberholster, Anna-Maria De Jager, Nicholas Stratos |
| author_facet | Botha-Oberholster, Anna-Maria De Jager, Nicholas Stratos |
| author_sort | De Jager, Nicholas Stratos |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2021. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/124253 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:47:16.314Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/124253 A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria De Jager, Nicholas Stratos Botha-Oberholster, Anna-Maria Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Institute for Plant Biotechnology. Diuraphis noxia Russian wheat aphid Wheat crop yields Russian wheat aphid -- Genetics Plant-pathogen relationships Wheat -- Diseases and pests UCTD Thesis (MScAgric)--Stellenbosch University, 2021. 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. AFRIKAANSE OPSOMMING: Diuraphis noxia (Kurdjumov, Hemiptera: Aphididae), algemeen bekend as die Russiese koringluis (RWA), is 'n floëemvoedende plaag wat ernstige skade aan die opbrengs van koring kan veroorsaak. Vinnige biotipe-vorming van hierdie plantluis is in die Verenigde State en Suid-Afrika, gedokumenteer. Hierdie biotipe-vorming veroorsaak die afbraak van weerstand in kommersiële RWA-weerstandige kultivars. Daar word bespiegel dat verskille in DNS-metileringpatrone geneties soortgelyke RWA's toelaat om meer virulent te word. Daarbenewens is bewys dat plantluis- geassosieerde bakterieë plantluisvirulensie in koring (Triticum aestivum L) vergemaklik. Om vas te stel of hierdie bakterieë die DNS-metileringpatroon in RWA-biotipes [US1 (saamgevoer); US2 (saamgevoer); US2 (geïsoleer)] beïnvloed, dus ook die virulensie van hierdie biotipes, is die DNS- metileringsprofiele en globale DNA-metilering- en hidroksimetilerings (5mC + 5hmC)-vlakke ondersoek. Dit is gedoen met behulp van metilering sensitiewe versterkte polimorfisme (MSAP)- en ensiem-gekoppelde immunosorberende toets (ELISA)-metodes, onderskeidelik. Boonop is die hele genoom-bisulfiet volgorde bepaling (WGBS) van hierdie biotipes uitgevoer, en is die konteks (CpG, CHH, CHG) van DNS-metilering met behulp van 'n gemodifiseerde Bismark-pyplyn bepaal. Verder is differensieel gemetileerde gene (DMG's) met behulp van die Bioconductor DSS (Dispersion Shrinkage for Sequencing data)-pakket geanaliseer. Die resultate van die MSAP- en ELISA-metodes dui daarop dat daar verskille in die DNS-metileringsprofiele van die biotipes was, wat daarop dui dat geassosieerde bakterieë die metilering in die RWA beïnvloed. Die WGBS-data het aan die lig gebring dat oor die algemeen, in elke konteks en streek, die minder virulente biotipes [US1 (saamgevoer); US2 (geïsoleer)] meer gemetileer (en minder gehemimetileer) was as die meer virulente biotipe [US2 (saamgevoer)], wat vorige bevindings oor RWA's bevestig het. Meer DMG's is gevind tussen die geïsoleerde en saamgevoerde US2-biotipes as US1 (saamgevoed) en US2 (saamgevoed), wat daarop dui dat plantluisverwante bakterieë 'n groot uitwerking op geenmetilering het. Tussen beide vergelykings was verskeie DMG's betrokke by lipiedmetabolisme en energieregulering, en sommige is geïdentifiseer om betrokke te wees by reaktiewe-suurstof species (ROS)-detoksifisering, verdedigingssein tydens mikrobiese inval en sterolomskakeling, wat dui op interaksies tussen die plantluis en die gepaardgaande bakterieë. Laastens is vyf potensiële effektore, deur gebruik te maak van 'n pasgemaakte effektorvoorspellingspyplyn, voorspel. Masters 2021-12-02T08:17:06Z 2022-02-22T10:20:11Z 2021-12-02T08:17:06Z 2021-12 Thesis http://hdl.handle.net/10019.1/124253 en_ZA Stellenbosch University xxxi, 238 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Diuraphis noxia Russian wheat aphid Wheat crop yields Russian wheat aphid -- Genetics Plant-pathogen relationships Wheat -- Diseases and pests UCTD De Jager, Nicholas Stratos A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria |
| title | A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria |
| title_full | A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria |
| title_fullStr | A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria |
| title_full_unstemmed | A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria |
| title_short | A comprehensive comparison of the methylomes between three Russian wheat aphid biotypes differing in virulence and associated bacteria |
| title_sort | comprehensive comparison of the methylomes between three russian wheat aphid biotypes differing in virulence and associated bacteria |
| topic | Diuraphis noxia Russian wheat aphid Wheat crop yields Russian wheat aphid -- Genetics Plant-pathogen relationships Wheat -- Diseases and pests UCTD |
| url | http://hdl.handle.net/10019.1/124253 |
| work_keys_str_mv | AT dejagernicholasstratos acomprehensivecomparisonofthemethylomesbetweenthreerussianwheataphidbiotypesdifferinginvirulenceandassociatedbacteria AT dejagernicholasstratos comprehensivecomparisonofthemethylomesbetweenthreerussianwheataphidbiotypesdifferinginvirulenceandassociatedbacteria |