Tshisekedi, Kalonji Abondance2022-08-012022-08-012021https://hdl.handle.net/10539/33082A dissertation submitted in fulfilment of the requirements for the degree Master of Science (in Molecular and Cell Biology) in the Faculty of Science, University of the WitwatersrandThe genus Naganishiawas recently re-established with the aim of addressing the diversity and heterogeneity of the yeast genus Cryptococcus. Many members of this genus have been isolated from harsh terrestrial conditions, including the dry cold valleys of Antarctica and the Atacama Desert. As a result, they have developed adaptive strategies to deal with the stressors associated with cold environments, such as desiccation, reduced availability of water, low availability of nutrients, high levels of ultraviolet (UV) radiation, high or low pH, and high osmotic pressure. Clinical manifestations of Naganishia species often include cutaneous lesions, encephalitis, keratitis, onychomycosis, and pneumonia. Members of this genus also have significant biotechnological value due to their capability to produce single cell oils (SCOs) and cold-active enzymes, which can be used in a variety of biotechnological and industrial applications that require low operating temperatures .Despite their potential biotechnological, environmental, and medical importance, the mechanisms underlying the diverse functions of Naganishia species remains poorly understood. In this study, we present the first genome sequence of N. randhawaeeABCC1, which was isolated from avian guano in South Africa. The genome of this strain was further explored using comparative genomic and phylogenomic analysis. The relevant literature on the taxonomy, ecology, and pathogenicity of Naganishia spp. is reviewed in Chapter 1. A comprehensive taxonomic history of the genus Naganishia is followed by an overview of the different ecological niches, with an emphasis on extreme ecosystems. Finally, biotechnological importance, clinical manifestations and factors that contribute to Naganishia pathogenicity are addressed. In Chapter 2, sequencing of N. randhawaeeABCC1 was performed using the Illumina NovaSeq 6000 platform (paired end read approach 2 X 250 bp) at MR DNA (Texas, USA). Subsequently, de novo assembly was undertaken, yielding a draft genome assembly comprised of 386 contigs, which was then structurally and functionally annotated. Two putative laccases were identified in the genomic content of N. randhawae eABCC1, which may be related to the development of melanin observed on bird seed agar (BSA).Furthermore, several putative pathogenicity determinants were identified in N. randhawae eABCC1. In Chapter 3, a comparative genome analysis of N. randhawae eABCC1 with N. albida strains JCM2334 and NT2002, as well as N. vishniacii ANT03-052,is presented. The pan-genome and its core and accessory elements were analysed at the protein level. These pan-genome fractions were further functionally characterised and categorised according to their Conserved Orthologous Groups (COGs). Finally, the annotated genomes of the four Naganishia strains were screened for metabolic pathways and genes involved in general stress response. Comparative genome analysis of the Naganishia pan genome revealed adaptation strategies hinting towards a role in multiple stress resistance. In Chapter 4, the phylogenomic analysis of 161 taxa within the class Tremellomycetes was performed. Single copy orthologues (SCOs) conserved among all the sampled taxa were identified, aligned and concatenated, before the generation of amaximum likelihood (ML) phylogeny. Taxonomic considerations included the proposal of a new order for the family Phaeotremellaceae (Phaeotremellaceales ord. nov.) and two new species combinations: Apiotrichum oleaginum comb. nov. and Naganishia frigoris comb. nov. Overall, findings from this study could pave the way for future phylogenomic studies of fungi at higher taxonomic ranks.enThesis