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Draft assembly of the Acacia mearnsii genome
Dissertation (MSc (Bioinformatics))--University of Pretoria, 2024.
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University of Pretoria
2025
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| _version_ | 1867613535075303424 |
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| access_status_str | Open Access |
| author2 | Naidoo, Sanushka |
| author_browse | Naidoo, Sanushka |
| author_facet | Naidoo, Sanushka |
| collection | Thesis |
| dc_rights_str_mv | © 2024 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 (Bioinformatics))--University of Pretoria, 2024. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/103601 |
| institution | University of Pretoria (South Africa) |
| last_indexed | 2026-06-10T12:37:41.144Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| 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:2263/103601 Draft assembly of the Acacia mearnsii genome Naidoo, Sanushka mondlixaba2@gmail.com Myburg, Alexander A Joubert, Fourie Duong, T. Xaba, Mondli Audrey UCTD Sustainable Development Goals (SDGs) Acacia mearnsii Long read sequencing Genome assembly Oxford nanopore De novo Dissertation (MSc (Bioinformatics))--University of Pretoria, 2024. A. mearnsii is an important forestry crop in South Africa occupying 7% of South Africa’s forestry estate. Despite its importance in the wood fibre and tannin industries and the rich history of wattle breeding in the country, there are still limited genomic resources for black wattle. Using high-molecular-weight DNA extraction methodology and data produced on a state-of-the-art long-read sequencing platform (Oxford Nanopore Technologies PromethION), we assessed the performance of three long-read genome assemblers for high-quality draft genome assembly of black wattle. We obtained 160 Gbp of sequencing data on a single PromethION flow cell, which amounts to 230X coverage of the black wattle genome (assuming a genome size of 686 Mbp). We produced a draft genome assembly comprising 430 contigs, with a contig N50 value of 2.3 Mbp, a total assembly size of 686 Mbp and a BUSCO (plant conserved single copy orthologs) completion score of 96.9%. De novo gene annotation identified 51,190 genes in the genome, with 62% of the genome marked as repeat content. We used single copy orthologs and a complete chloroplast genome assembly to assess the phylogenetic history of black wattle in relation to other plant taxa. Using in silico approaches, we have also identified microsatellite DNA loci and used these for the development of oligonucleotide primers for DNA fingerprinting and parentage analyses in wattle breeding. This study demonstrated the efficiency of long-read DNA sequencing technology and current genome assemblers in producing a high-quality de novo draft genome assembly for A. mearnsii, which will serve as a reference for future studies of genome biology and genetic dissection of agronomic traits in black wattle. Institute for Commercial Forestry Research (ICFR) NCT Forestry Agricultural Co-operative Limited Biochemistry, Genetics and Microbiology (BGM) MSc (Bioinformatics) Unrestricted Faculty of Natural and Agricultural Sciences SDG-09: Industry, innovation and infrastructure 2025-07-25T09:22:55Z 2025-07-25T09:22:55Z 2025-09 2024-11 Dissertation * S2025 http://hdl.handle.net/2263/103601 https://doi.org/10.25403/UPresearchdata.29634194 © 2024 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) Acacia mearnsii Long read sequencing Genome assembly Oxford nanopore De novo Draft assembly of the Acacia mearnsii genome |
| title | Draft assembly of the Acacia mearnsii genome |
| title_full | Draft assembly of the Acacia mearnsii genome |
| title_fullStr | Draft assembly of the Acacia mearnsii genome |
| title_full_unstemmed | Draft assembly of the Acacia mearnsii genome |
| title_short | Draft assembly of the Acacia mearnsii genome |
| title_sort | draft assembly of the acacia mearnsii genome |
| topic | UCTD Sustainable Development Goals (SDGs) Acacia mearnsii Long read sequencing Genome assembly Oxford nanopore De novo |
| url | http://hdl.handle.net/2263/103601 https://doi.org/10.25403/UPresearchdata.29634194 |