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Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus)
Thesis (MScAgric)--Stellenbosch University, 2025.
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| Format: | Thesis |
| Language: | English |
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613772185600000 |
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| access_status_str | Open Access |
| author | Roux, Mariek |
| author2 | Rhode, Clint |
| author_browse | Rhode, Clint Roux, Mariek |
| author_facet | Rhode, Clint Roux, Mariek |
| author_sort | Roux, Mariek |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/133122 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:41:26.849Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/133122 Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) Roux, Mariek Rhode, Clint Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics & Institute of Plant Biotechnology. Argyrosomus Argyrosomus japonicus -- South Africa Fishes -- Genetics Genomics Gene expression UCTD Thesis (MScAgric)--Stellenbosch University, 2025. Roux, M. 2025. Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus). Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available:https://scholar.sun.ac.za/items/1abab1f2-56ce-4ab6-bd55-837ae52c2d3e ENGLISH ABSTRACT: Argyrosomus japonicus (dusky kob) is an aquaculture species with high commercial value in South Africa, for which a draft genome is available. Repetitive elements are non-genic sequences that occur as repeats throughout the genome, generally classified as either tandem repeats or transposable elements (TEs). In this study, repetitive elements were characterised in A. japonicus, with a main focus on TEs. The total repeat composition of the genome was determined to be 25.81%. The two major TE classes, DNA transposons and retrotransposons, contributed 11.09 and 10.93%, respectively. For tandem repeats, 16 and 15 satellite DNA (satDNA) families were identified in male and female sequence data, respectively. Integrating the tandem repeat and TE datasets, an LTR/Copia TE was identified that consisted mainly of tandem repeats, highlighting the potential overlap between tandem repeats and transposable elements. The genomes of the South African and Chinese A. japonicus conspecifics, three other sciaenid species (Argyrosomus regius, Larimichthys crocea and Nibea albiflora) and Danio rerio were compared in terms of TE content and TE divergence distributions. This revealed notable differences, and the TE divergence data shed light on the unique genomic histories of these species. To further investigate TE characteristics and their potential functional impact, transcriptional analysis of TEs were performed for A. japonicus. The RNA-seq data of muscle, liver, and gill tissues were used for differential expression analyses of TEs. Results showed clear tissue-specific transcriptional activity of certain TE types – LTR/Copia was linked to liver tissue, LTR/Gypsy and DNA/TcMar to muscle tissue, and DNA/CACTA to gill tissue. Furthermore, TEs were characterised with regards to their distance to genes, revealing that 34% of TEs were located within genes. Select TE-gene pairs were also assessed for expression correlation. Interestingly, a DNA/TcMar copy residing within gene myhz1.2_a was found to be correlated in expression levels to gene myhz1.2_b, in muscle tissue. Since these genes are involved in muscle function, this suggests the potential functional relevance of this TE copy. Overall, this study contributes to knowledge of the evolutionary and functional importance of TEs, and repetitive elements in general. AFRIKAANSE OPSOMMING: Argyrosomus japonicus, ook bekend as die boer-kabeljou, is ‘n akwakultuur spesie van kommersiële belang in Suid-Afrika, waarvoor daar reeds ’n konsepgenoom beskikbaar is. Herhalende elemente is nie-geniese volgordes wat herhalend regoor die genoom gevind kan word. Hulle word algemeen geklassifiseer as of tandemherhalings of verskuifbare elemente (VEs). Die doel van hierdie studie was om herhalende elemente in A. japonicus te karakteriseer, met die VEs as die hooffokus. Die totale herhalingsamestelling van die genoom is bepaal as 25.81%, en die twee hoof VE klasse, DNS verskuifbare elemente en retro-verskuifbare elemente, het onderskeidelik 11.09 en 10.93% van die totaal opgemaak. Onder die tandemherhalings was daar onderskeidelik 16 en 15 satelliet DNS (satDNS) families geïdentifiseer in die manlike en vroulike volgorde data. Daar was ook ‘n LTR/Copia VE geïdentifiseer wat hoofsaaklik uit tandemherhalings bestaan het, en hierdie bevinding beklemtoon die potensiële oorvleueling tussen VEs en tandemherhalings. Die genome van beide die Suid Afrikaanse en die Chinese A. japonicus soortgenote, sowel as die van drie ander sciaenid spesies (Argyrosomus regius, Larimichthys crocea, Nibea albiflora), en Danio rerio was vergelyk om te sien hoe en of hulle VE inhoud en VE divergensie verskil. Noemenswaardige verkille was uitgelig, en die VE divergensie data het die unieke genomiese geskiedenisse van die spesies aan die lig gebring. Om verder die eienskappe en potensiële funksionele impak van VEs te ondersoek, was daar ’n transkripsionele analise uitgevoer vir A. japonicus. Die RNS-volgorde data van weefsels van die spiere, lewer, en kieue was gebruik om differensiële uitdrukking analises van die VEs uit te voer. Die resultate het getoon dat daar beduidende weefsel-spesifieke transkripsionele aktiwiteit van sekere VE tipes was, naamlik LTR/Copia in die lewerweefsel, LTR/Gypsy en DNA/TcMar in die spierweefsel, en DNA/CACTA in die kieuweefsel. Die VEs was ook gekarakteriseer op grond van hul afstand vanaf gene, en geselekteerde VE-geen pare was geassesseer op grond van hul uitdrukkingskorrelasie. Daar was gevind dat 34% van die VEs binne gene geleë is. Interessant genoeg was daar ’n korrelasie tussen die uitdrukkingsvlakke van die myhz1.2_b geen en ‘n DNA/TcMar kopie wat binne die geen myhz1.2_a geleë is. Aangesien hierdie gene betrokke is in spierfunksie, kan dit ‘n aanduiding wees van die potensiële funksionele relevansie van hierdie VE kopie. As ‘n geheel dra hierdie studie by tot die kennis van die evolusionêre en funksionele belang van VEs asook herhalende elemente in die algemeen. Masters 2025-07-18T08:42:27Z 2025-07-18T08:42:27Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/133122 en Stellenbosch University xiv, iii, 96 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Argyrosomus Argyrosomus japonicus -- South Africa Fishes -- Genetics Genomics Gene expression UCTD Roux, Mariek Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) |
| title | Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) |
| title_full | Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) |
| title_fullStr | Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) |
| title_full_unstemmed | Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) |
| title_short | Characterisation of repetitive elements in dusky kob (Argyrosomus japonicus) |
| title_sort | characterisation of repetitive elements in dusky kob argyrosomus japonicus |
| topic | Argyrosomus Argyrosomus japonicus -- South Africa Fishes -- Genetics Genomics Gene expression UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/133122 |
| work_keys_str_mv | AT rouxmariek characterisationofrepetitiveelementsinduskykobargyrosomusjaponicus |