Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
Comparative genomics of diverse African isolates of Cercospora zeina
Thesis (PhD (Bioinformatics))--University of Pretoria, 2024.
Saved in:
| Other Authors: | |
|---|---|
| Format: | Thesis |
| Language: | English |
| Published: |
University of Pretoria
2024
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613672174518272 |
|---|---|
| access_status_str | Open Access |
| author2 | Berger, David Kenneth |
| author_browse | Berger, David Kenneth |
| author_facet | Berger, David Kenneth |
| collection | Thesis |
| dc_rights_str_mv | © 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Thesis (PhD (Bioinformatics))--University of Pretoria, 2024. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/96745 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:39:52.104Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/96745 Comparative genomics of diverse African isolates of Cercospora zeina Berger, David Kenneth u13044542@tuks.co.za Duong, Tuan A. Barnes, Irene Stukenbrock, Eva H. Welgemoed, Tanya UCTD Sustainable development goals (SDGs) Maize Grey leaf spot disease Cercospora zeina Population genomics Pangenome Crop pathogen SDG-02: Zero hunger Natural and agricultural sciences theses SDG-02 Thesis (PhD (Bioinformatics))--University of Pretoria, 2024. A serious factor hampering global maize production is grey leaf spot disease. Cercospora zeina is the causative pathogen in Africa, but population genomics analysis of C. zeina is lacking. The literature was reviewed for genomics-based management of African cereal crop pathogens. Whole-genome Illumina sequencing and de novo genome assembly was conducted on a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the assembled genomes and the published long-read C. zeina reference assembly (CMW25467) was done through protein clustering. This revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). SNP analysis through PCA, ADMIXTURE, and neighbour-net network phylogeny, revealed a population structure with geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. Accessory gene content was however largely shared between isolates from all countries, with few genes unique to Southern Africa (32) or East Africa (6). Selective sweep detection revealed selective sweeps in East Africa (20) and Southern Africa (24), within which were six effector genes. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa. University of Pretoria National Research Foundation Biochemistry PhD (Bioinformatics) Unrestricted Faculty of Natural and Agricultural Sciences SDG-02: Zero Hunger 2024-07-01T14:30:52Z 2024-07-01T14:30:52Z 2024-09 2024-06 Thesis * S2024 http://hdl.handle.net/2263/96745 DOI: https://doi.org/10.25403/UPresearchdata.22987640.v1 https://doi.org/10.25403/UPresearchdata.22987640 en © 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | UCTD Sustainable development goals (SDGs) Maize Grey leaf spot disease Cercospora zeina Population genomics Pangenome Crop pathogen SDG-02: Zero hunger Natural and agricultural sciences theses SDG-02 Comparative genomics of diverse African isolates of Cercospora zeina |
| title | Comparative genomics of diverse African isolates of Cercospora zeina |
| title_full | Comparative genomics of diverse African isolates of Cercospora zeina |
| title_fullStr | Comparative genomics of diverse African isolates of Cercospora zeina |
| title_full_unstemmed | Comparative genomics of diverse African isolates of Cercospora zeina |
| title_short | Comparative genomics of diverse African isolates of Cercospora zeina |
| title_sort | comparative genomics of diverse african isolates of cercospora zeina |
| topic | UCTD Sustainable development goals (SDGs) Maize Grey leaf spot disease Cercospora zeina Population genomics Pangenome Crop pathogen SDG-02: Zero hunger Natural and agricultural sciences theses SDG-02 |
| url | http://hdl.handle.net/2263/96745 https://doi.org/10.25403/UPresearchdata.22987640 |