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Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations
Dissertation (MSc)--University of Pretoria, 2013.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2014
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| _version_ | 1867613725944446976 |
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| access_status_str | Open Access |
| author2 | Pietersen, Gerhard |
| author_browse | Pietersen, Gerhard |
| author_facet | Pietersen, Gerhard |
| collection | Thesis |
| dc_rights_str_mv | © 2013 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)--University of Pretoria, 2013. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/33177 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:40:43.223Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| 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:2263/33177 Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations Pietersen, Gerhard ozablocki@hotmail.com Zablocki, Olivier Citrus tristeza virus Citrus sinensis UCTD Dissertation (MSc)--University of Pretoria, 2013. A high-throughput sequencing pipeline to characterize Citrus tristeza virus isolates was developed. Three alternative viral templates (total RNA, double-stranded RNA and virus particles) were first tested on a single, previously characterized GFMS12 sub-isolate for their enrichment qualities, and combined with random RT-PCR amplification were subjected to Illumina paired-end sequencing. Double-stranded RNA was found to be most useful and was selected for further characterization of additional isolates (glasshouse-kept and field-derived). A novel South African genotype, named CT-ZA3 was assembled de novo and shown to be the dominant component in all GFMS12 sub-isolates tested. Genotype distributions within field-derived isolates collected from commercial orange (Citrus sinensis) orchards revealed a mixed infection status, dominated by a resistance breaking (RB)-like component (Tai-SP) coupled with a minor, VT-like (mild) (Kpg3) component. Based on read mapping patterns from field isolates, it is further suggested that two previously unknown recombinants may be present: a SP/Kpg3 and HA16-5/Kpg3 combination. This study underlined the effectiveness of next-generation sequencing for genotype discovery as well as whole-genome characterization of CTV isolates to a level of detail previously unreachable with classical methods such as SSCP and Sanger sequencing of multiple clones. gm2014 Microbiology and Plant Pathology unrestricted 2014-01-28T14:27:49Z 2014-01-28T14:27:49Z 2013-09-06 2013 Dissertation Zablocki, ODJ 2013, Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations, MSc dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/33177> E13/9/2013 http://hdl.handle.net/2263/33177 en © 2013 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 | Citrus tristeza virus Citrus sinensis UCTD Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations |
| title | Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations |
| title_full | Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations |
| title_fullStr | Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations |
| title_full_unstemmed | Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations |
| title_short | Unbiased, next-generation sequencing for the characterization of Citrus tristeza virus populations |
| title_sort | unbiased next generation sequencing for the characterization of citrus tristeza virus populations |
| topic | Citrus tristeza virus Citrus sinensis UCTD |
| url | http://hdl.handle.net/2263/33177 |