Repeat-induced point mutations in the Fusarium fujikuroispecies complex

Abstract

The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defence mechanism that mitigates the deleterious consequences of repeated motifs and transposable elements (TEs). RIP is an ancient pathway that evolved early in the evolutionary history of fungi. It most likely evolved before the divergence of the fungal subkingdom Dikarya and has been observed in both Ascomycota and certain Basidiomycota. Despite its prevalence, the genetic consequences and taxonomic range of RIP remains ill defined. For these reasons this thesis particularly focusses on fungi representing varying degrees of divergence in order to investigate the influence of RIP on genome evolution, divergence and development of genomic regions underlying important fungal biological traits. The Fusarium fujikuroi species complex (FFSC) represents a diverse assemblage of fungi that are distributed globally. Many of these fungi can cause disease on numerous crops and plants and threaten tree health in both natural and plantations settings. Due to their agricultural importance, and the biological and genomic interest in this taxon, whole genome sequences have been determined for many FFSC species. The availability of this information assembled into chromosome-sized scaffolds allows for unique opportunities to study the occurrence and extent of RIP on a genome-wide level. Moreover, the availability of these genomes, in varying stages of divergence, will prove invaluable in the understanding of the genetic and molecular factors driving genome evolution, lineage divergence, and ultimately speciation. The first chapter of this thesis is a critical review of the literature on the developments made in studying the RIP process in fungi. The different aspects of fungal biology and genome content that can contribute to variation in RIP strength and capabilities are discussed. As this thesis deals with the evolutionary implications of RIP on the FFSC, the current research progress made on RIP in Fusarium lineages is reviewed. Attention is also given to the functional consequences brought about by RIP, particularly how RIP can contribute to reinforcing species boundaries and ultimately drive lineage divergence and speciation. Chapter two introduces The RIPper, a web-based set of tools for genome-wide investigation of RIP in fungi in the phylum Ascomycota. This chapter discusses the development of this software and further demonstrates the ability of this set of software tools to detect the occurrence and extent of RIP in known RIP affected fungal sequences. The work presented in xix Chapter 2 has been published in the journal PeerJ as an application for genome-wide RIP analyses of fungal sequences. Chapter three presents detailed investigation on the extent and occurrence of RIP in the genome of the pitch canker pathogen, Fusarium circinatum and its relatives in the FFSC. Comparative genome-wide RIP analyses were undertaken to determine the influence of RIP on genome divergence amongst these fungi. This chapter provides valuable information on the independent divergence of chromosomes and changes to chromosome architecture brought about by RIP among this economic important group of fungi. The work presented was published in the journal Pathogens. Fusarium pininemorale is a recently recognized member of the American clade of the FFSC and is the focus of chapter 4. Overall, little is known regarding the biology and genetics of this species, even less so for the genetic determinants of host range in the broader American clade of the FFSC. The aim of chapter four was to determine the full genome sequence for F. pininemorale which will allow further studies to investigate genomic aspects of not only genome evolution but will also provide information of its biology and evolution amongst members of the FFSC. The chapter has been published in the journal IMA Fungus. In chapter 5 data on the genome-wide occurrence and extent of RIP in the Ascomycota is presented. This study considered the effects of the RIP amongst these fungi using whole genome sequences. To overcome the typical challenges associated with RIP analyses, genomewide RIP data is produced by using an alignment-free method, based on a sliding-window approach. This study provides valuable information on the taxonomic distribution of RIP amongst the Ascomycetes, occurrence and extent of RIP in regions with TEs and repeats, as well as where RIP occurred due to leakage. This work provides valuable insights on the cumulative influence of RIP and its contribution to chromosome evolution of Ascomycete fungi. This chapter has been submitted to the journal Microorganisms for peer review. The cumulative influence of RIP on the overall base composition in the different genomic regions and sub-genomic compartments of F. circinatum is the focus of chapter six. The results of this study present important information on the manner that RIP drives genomic variation and contributes to the evolution of the genetic landscape and differentiation of diverse sub-genomic compartments of this important fungal pathogen.