Genome defence mechanisms in Basidiomycota fungi, with special reference to Armillaria species

Abstract

Chapter One of this dissertation presents a literature review of aspects of TEs and their important roles in the genome evolution of Basidiomycota and other fungi. The genome defence mechanisms that prevent the expansion and deleterious activity of TEs in fungi are also reviewed. Additionally, the biology, occurrence, and genome evolution of Armillaria species are discussed. Chapter Two deals with research on the occurrence of the RIP mutations and the RIP pathway in selected Armillaria species and related fungi in the Agaricales, the order in which Armillaria species reside. This was achieved by using bioinformatics methods that included a sliding-window approach and alignment-based RIP analyses. The key genes encoding RID (RIP deficient) and DIM-2 (defective in methylation 2) cytosine methyltransferases involved in the RIP process, and those implicated in the MIP process Masc-1 (Methyltransferase from Ascobolus 1) and Masc-2 cytosine methyltransferases were investigated. The findings of this study will contribute to the existing body of knowledge on the taxonomic distribution of RIP in Basidiomycota and its preferred genetic mutation targets. Chapter Three focused on the identification and characteristics of the RNAi pathway genes in Armillaria species and other species from the family Physalacriaceae that previously were shown to employ the RIP mutation mechanism. In addition, the evolution of these genes in relation to other representative species in the Basidiomycota was investigated. This was achieved by performing sequence similarity comparisons, searches for the conserved functional domains of the genes and phylogenetic analysis. The findings from this study lay the foundation for future studies that will focus on characterizing the potential roles of these genes in response to genome defence against TEs in these species.