Ceratocystis fimbriata is the type species for the genus Ceratocystis and was first described as the causal agent of black rot in sweet potatoes. However, evidence from DNA sequence data suggests that C. fimbriata is in fact a species complex (C. fimbriata sensu lato) consisting of many morphologically similar cryptic species. Species in this complex are pathogens of important root and fruit crops and trees in the forestry industry world-wide. Population studies on some of these species have mainly relied on microsatellite markers. However, nothing is known regarding the microsatellite structure within Ceratocystis species or any species in the order Microascales in which Ceratocystis resides. The need for a more robust identification tool is also required to differentiate between species in this complex. The first chapter of this thesis provides a review of the literature on microsatellite markers, particularly in fungi. It also discusses the history of microsatellites, mechanisms of microsatellite evolution and functional importance in selected fungal examples. In addition, isolation methodologies are compared and contrasted to newly developed techniques that include bioinformatic searches of genome sequences. Opportunities to use and develop microsatellite markers in Ceratocystis species is also discussed with an emphasis on the possibilities that more microsatellites markers would provide. Microsatellites are abundant in eukaryotic genomes, and fungi are no exception. Analyses of microsatellite content in eukaryotic and fungal genomes have shown that fungi contain fewer microsatellites and that each organism shows preference for particular motifs. In Chapter 2 of this thesis, the abundance and distribution of microsatellites in the recently sequenced C. fimbriata genome is investigated. Comparisons to other fungi and eukaryotes show that C. fimbriata follows the general pattern of microsatellite structure, however it is unique in its preference for certain motifs. The C. fimbriata sensu lato species complex contains morphologically indistinct species. Microsatellite markers previously developed for a population study could differentiate between some of the cryptic species based on their geographic location and host-specificity. In Chapter 3 a subset of microsatellite markers identified in gene regions in Chapter 2 are used to develop a diagnostic test to differentiate between species in the complex. Microsatellite markers that are polymorphic between species but monomorphic within species were selected for this purpose. However, not all species could be distinguished using this diagnostic test. This thesis is presented as a series of chapters in which Chapters 3 2 and 3 are in manuscript format. Consequently each chapter represents an independent article and repetition between these chapters has been unavoidable. / Dissertation (MSc)--University of Pretoria, 2014. / Genetics / Unrestricted

Le travail effectué dans cette thèse présente une nouvelle approche de la théorie du code circulaire dans les gènes qui a été initiée en 1996. Cette approche consiste à analyser les motifs construits à partir de ce code circulaire, ces motifs particuliers sont appelés motifs de code circulaire. Ainsi, nous avons développé des algorithmes de recherche pour localiser les motifs de code circulaire dans les séquences d'acides nucléiques afin de leur trouver une signification bioinformatique. En effet, le code circulaire X identifie dans les gènes est un ensemble de trinucleotides qui a la propriété de retrouver, synchroniser et maintenir la phase de lecture. Nous avons commencé notre analyse avec le centre de décodage du ribosome (ARNr) qui est une région majeure dans le processus de traduction des gènes aux protéines. Puis, nous avons étendu les résultats obtenus avec le ribosome aux ARN de transfert (ARNt) pour étudier les interactions ARNr-ARNt. Enfin, nous avons généralisé la recherche de motifs de code circulaire X dans l'ADN aux chromosomes d'eucaryotes complets. / The work done in this thesis presents a new direction for circular code identified in 1996 by analysing the motifs constructed from circular code. These particular motifs are called circular code motifs. We applied search algorithms to locate circular code motifs in nucleic acid sequences in order to find biological significance. In fact, the circular code X, which was found in gene sequences, is a set of trinucleotides that have the property of reading frame retrieval, synchronization and maintenance. We started our study in the ribosomal decoding centre (rRNA), an important region involved in the process of translating genes into proteins. Afterwards, we expanded our scope to study the interaction of rRNA through the X circular code. Finally, we search for the X circular code motifs in the complete DNA sequences of chromosomes of the eukaryotic genomes. This study introduced new properties to the circular code theory.