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Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex
Dissertation (MSc (Genetics))--University of Pretoria, 2024.
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University of Pretoria
2024
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| _version_ | 1867613615561900032 |
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| access_status_str | Open Access |
| author2 | Duong, Tuan A. |
| author_browse | Duong, Tuan A. |
| author_facet | Duong, Tuan A. |
| collection | Thesis |
| dc_rights_str_mv | © 2021 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 | Dissertation (MSc (Genetics))--University of Pretoria, 2024. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/99649 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:38:57.791Z |
| 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:2263/99649 Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex Duong, Tuan A. deanne.duplessis@up.ac.za Wingfield, Brenda D. Wingfield, Michael J. Du Plessis, Deanne UCTD Comparative genomics Vascular wilt pathogens Laccase gene Pathogenicity genes Leptographium wageneri Dissertation (MSc (Genetics))--University of Pretoria, 2024. Fungal vascular wilt pathogens cause destructive diseases in many agriculturally important crop and tree species. Many of these pathogens are soil-borne and enter their hosts via pre-existing structures, or with the aid of insect vectors. However, there is remarkably little knowledge available regarding the molecular mechanisms of infection and pathogenicity in these fungi. Species in the Leptographium wageneri complex cause black stain root disease of conifers. This disease is characterised by black staining of the lower stems, roots, and tracheids, leading to wilt and tree death. There are three host specific species in the complex: L. wageneri, L. pseudotsugae and L. ponderosum. The genetic mechanisms underlying their pathogenicity and host adaptation have not been identified. To better understand potential pathogenicity associated factors, comparative genomic analysis was performed by comparing the genomes of species in the L. wageneri complex with those from related non-pathogenic species that reside in the same genus as well as genomes of pathogenic and non-pathogenic species in the Ophiostomataceae. The in vitro and in planta expression of an identified laccase gene was investigated to reveal its role in pathogenicity. Furthermore, laccasedeletion mutants were generated using the CRISPR-Cas9 gene editing system, followed by a pathogenicity trial on Pinus patula seedlings. Finally, a genome-wide approach was used to identify genomic regions under selection that might explain the host specialization in species of the L. wageneri complex. Genome sequences were generated for the three species in the L. wageneri complex and the nonpathogenic L. douglasii. The results revealed that species in the L. wageneri complex have larger genomes, higher gene numbers and a higher genome-wide content of transposable elements. Overall, both pathogenic and non-pathogenic species in the Ophiostomataceae have similar numbers of pathogenicity associated factors, such as secondary metabolite clusters, CAZymes, and effectors. Phylogenetic analyses indicated that the laccase gene has been horizontally acquired by species of the L. wageneri complex and L. douglasii. Expression analysis revealed that the laccase gene is up regulated in planta. The pathogenicity trial conducted with laccase-deletion mutants confirmed the essential role of the laccase gene in pathogenicity. Whole-genome SNP data were used to investigate the evolutionary relationships and genetic patterns of diversification between species of the L. wageneri complex. Structure analysis revealed three distinct clusters, each representing a species in the complex. Evolutionary analyses indicated that L. wageneri is more closely related to L. pseudotsugae, than to L. ponderosum. Selection analysis revealed several genomic regions underwent positive selection, that could explain their differentiation and host associations. Finally, I have discussed how genes within these genomic regions that encode for a heterochromatin incompatibility protein, a protein kinase and a Multi-drug transporter protein could underly the diversification and host specification in the species of the L. wageneri complex. Biochemistry, Genetics and Microbiology (BGM) MSc (Genetics) Unrestricted Faculty of Natural and Agricultural Sciences SDG-02:Zero Hunger 2024-11-28T06:53:38Z 2024-11-28T06:53:38Z 2024-09 2024 Dissertation * S2024 http://hdl.handle.net/2263/99649 10.25403/UPresearchdata.26335447 en © 2021 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 Comparative genomics Vascular wilt pathogens Laccase gene Pathogenicity genes Leptographium wageneri Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex |
| title | Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex |
| title_full | Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex |
| title_fullStr | Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex |
| title_full_unstemmed | Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex |
| title_short | Genomic insights into the pathogenicity and host adaptation in species of the Leptographium wageneri complex |
| title_sort | genomic insights into the pathogenicity and host adaptation in species of the leptographium wageneri complex |
| topic | UCTD Comparative genomics Vascular wilt pathogens Laccase gene Pathogenicity genes Leptographium wageneri |
| url | http://hdl.handle.net/2263/99649 |