Mr Riaan Swanepoel



PhD student

Department

Centre for Bioinformatics and Computational Biology
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Primary Supervisor
Eshchar Mizrachi

I started studying at the University of Pretoria in 2010 and graduated with a degree in Genetics in 2013. For my honours project in Bioinformatics, I characterized the gene structure and transcript diversity of 9 hymenopteran species in order to determine whether the evolution of eusociality and the increase of pathogenic pressures had a selective pressure on the diversity of immune-related genes.

For my masters project, I assessed and optimized the various components of de novo transcriptome assembly in non-model organisms and assessing their effects on the quality of the de novo assembled transcriptomes. This project aimed to provide an optimised SOP for assembling de novo transcriptomes and the assessment of these transcriptomes.

 

The exploitation of non-renewable fossil carbon-based resources is an unsustainable and often detrimental exercise as tonnes of non-degradable waste and pollutants accumulate in the environment. Crises such as these are driving the move towards a more bio-based economy, utilizing organic and sustainable natural products such as plant secondary metabolites, which will alleviate many of the detrimental effects of fossil carbon-based resources on the environment. The Cycadales is a group of primitive gymnosperms possessing many unique biological innovations. Furthermore, their remarkable resistance to disease and pests have been postulated to be due to the diversity and specialization of secondary metabolites. The lack of research and integration on the molecular level of cycad metabolism must be addressed to fully understand the development and evolution of the unique innovations of this lineage, and indeed all spermatophytes. The focus of my PhD is to use gene co-expression networks together with secondary metabolite data to determine the biosynthetic pathways of secondary metabolites that might be of industrial and economical importance within the cycad Encephalartos natalensis.

 

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Publication
Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. (2017) Evidence for an ancient whole genome duplication in the cycad lineage. PLOS ONE 12(9):e0184454. 10.1371/journal.pone.0184454