Systematic and genomic studies in the plant genus Zygophyllum
| dc.contributor.advisor | Bellstedt, D. U. | en_ZA |
| dc.contributor.advisor | Pirie, Michael David | en_ZA |
| dc.contributor.author | Van der Merwe, Pieter de Wet | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of Science. Dept. of Biochemistry. | en_ZA |
| dc.date.accessioned | 2015-05-20T09:28:05Z | |
| dc.date.available | 2015-05-20T09:28:05Z | |
| dc.date.issued | 2015-04 | en |
| dc.description | Thesis (MSc)--Stellenbosch University, 2015. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: Zygophyllum orbiculatum Welwitsch ex Oliv. from Angola and Zygophyllum stapffii Schinz from Namibia were described in the late 1800’s. Recent comparisons of these two species revealed that they were morphologically very similar except that Zygophyllum orbiculatum has unifoliolate leaves and Zygophyllum stapffii has bifoliolate leaves. The similarity of these two species was investigated using nuclear ITS (Internal Transcribed Spacer, i.e. ITS1, 5.8SrDNA, ITS2) region sequence data as phylogenetic markers. Due to almost identical sequences and phylogenetic grouping, it was concluded that they were conspecific. However, the phylogenetic relationships of the major groups within the subfamily Zygophylloideae based on ITS sequences, were unresolved and unsupported, as was found in previous studies using chloroplast gene marker sequences. To resolve the phylogenetic relationships of the major groups within the subfamily Zygophylloideae, a next generation sequencing (NGS) approach was taken. Chloroplasts of taxa representing the major groups within the subfamily were isolated and chloroplast genome sequence data were generated using the Ion Torrent™ sequencer. Additional nuclear ITS cassette data (18SrDNA, ITS1, 5.8SrDNA, ITS2, 26SrDNA) were generated as a by-product and used to produce a large combined aligned sequence matrix for phylogenetic analysis. Model-based phylogenetic programs were able to retrieve strongly supported and resolved phylogenetic relationships of the major groups within Zygophylloideae. Two basal groupings were retrieved in the subfamily. The first grouping consisted of the genera Tetraena, Fagonia and Melocarpum. The second grouping consisted of the monotypic genus Augea and Zygophyllum orbiculatum/stapffii which were embedded within the genus Roepera. Using a gene duplication approach, the chloroplast marker data of genus Zygophyllum sensu stricto placed this genus basal to the Augea, Zygophyllum orbiculatum/stapffii, Roepera clade whilst the nuclear marker data of Zygophyllum sensu stricto, was found in a basal position to the entire subfamily. From this it is concluded that Zygophyllum sensu stricto shows evidence of incomplete lineage sorting. A revised taxonomy for the entire subfamily Zygophylloideae is proposed. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Zygophyllum orbiculatum Welwitsch ex Oliv. uit Angola en Zygophyllum stapffii Schinz van Namibië is in die laat 1800's beskryf. Onlangse vergelykings van hierdie twee spesies het getoon dat hulle morfologies baie eners is, behalwe dat Zygophyllum orbiculatum unifoliolate blare besit en dat Zygophyllum stapffii bifoliolate blare besit. Hierdie ooreenkoms is ondersoek, met behulp van die nukleêre “ITS” (Internal Transcribed Spacer d.w.s. ITS1, 5.8SrDNA, ITS2) DNS-strook volgordedata as filogenetiese merkers. As gevolg van feitlik identiese geenopeenvolgings is bevind dat die twee spesies konspesifiek is. Die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae, gebaseer op ITS geenopeenvolgings, was egter onopgelos en nie ondersteun nie, net soos in vorige studies waarin chloroplast geenmerkervolgordes gebruik was. Om die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae op te los, was ‘n betreklik nuwe DNS volgordebepalingstegniek, naamlik “Next Generation Sequencing” (NGS), gebruik. Chloroplaste van taksa, wat die groot groepe binne-in die subfamilie verteenwoordig, is geïsoleer en chloroplast genoomdata is gegenereer met behulp van die Ion Torrent ™ (NGS) DNS-volgordebepaler. Bykomend was die nukleêre “ITS”-kasset volgordedata (18SrDNS, ITS1, 5.8SrDNS, ITS2, 26SrDNS) ook as 'n by-produk gegenereer en ook gebruik om 'n groot gesamentlike DNS oplyningmatriks vir filogenetiese doeleindes. Model-gebaseerde filogenetiese programme was in staat was om sterk ondersteuning en opgeloste filogenetiese verwantskappe van die groot groepe binne-in Zygophylloideae te ontravel. Die subfamilier toon twee basale groeperinge. Die eerste groepering bestaan uit die genera Tetraena, Fagonia en Melocarpum. Die tweede groepering bestaan uit die monotipiese genus Augea en Zygophyllum orbiculatum/stapffii, wat ingebed is binne-in die genus Roepera. Deur ‘n geendupliseringsbenadering te gebruik op die DNS geenopeenvolgings van die verteenwoordigende takson van Zygophyllum sensu stricto, is bevind dat die chloroplast DNS volgordes hierdie groep basaal aan ‘n Roepera/Augea/Zygophyllum orbiculatum/stapffii klade plaas, terwyl die nukleêre DNS volgordes hierdie groep basaal aan die hele subfamilie Zygophylloideae plaas. Hieruit is die gevolgtrekking gemaak dat Zygophyllum sensu scricto bewyse van onvolledige afstammelingsortering toon. ‘n Gewysigde taksonomie vir die hele subfamilie Zygophylloideae word voorgestel. | af_ZA |
| dc.format.extent | x, 193 pages : colour illustrations | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/96877 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Zygophyllaceae | en_ZA |
| dc.subject | Genomics | en_ZA |
| dc.subject | Nucleotide sequence | en_ZA |
| dc.subject | UCTD | |
| dc.title | Systematic and genomic studies in the plant genus Zygophyllum | en_ZA |
| dc.type | Thesis | en_ZA |