Mitochondrial genomes from the Ceratocystidaceae and species boundaries in Ceratocystis

The fungal family Ceratocystidaeceae contains several genera that are considered highly pathogenic and able to cause disease on a wide range of hosts. The taxonomic history of Ceratocystidaceae species has been under debate for many years due to the lack of morphologically distinguishing characteristics between the species and genera. Chapter one of this thesis provides a broad overview of the speciation process from defining species to studying the barriers that prevents gene flow between populations or prevents hybrid zygotes from developing before and/or after fertilization. Different speciation genomic approaches, their advantages and limitations are also discussed. The chapter also provides a brief overview of the taxonomy, species delineation and the controversies associated with this process in the Ceratocystidaceae, focusing specifically on the Ceratocystis fimbriata sensu lato complex. The second chapter presents the work on characterisation of mitochondrial (mt) genomes for 18 species in 10 genera in the Ceratocystidaceae. The aim of this chapter was thus to assemble, characterise and comparatively analyse mt genomes from multiple species and genera in the Ceratocystidaceae. The work of chapter 3 focuses on the taxonomic confusion that has historically plagued the C. fimbriata s.l complex. The aim of this chapter was to use whole genome SNP data from a large collection of isolates of C. fimbriata sensu lato complex to investigate species boundaries, phylogenetic relationships, and the genetic differentiation between these closely related species. Taken together, the body of the work presented in this dissertation contributes to the current understanding of mitochondrial genome evolution, species boundaries, and the evolutionary relationship among species and genera within the Ceratocystidaceae. These findings pave the way for future research aimed at exploring the biology, pathogenicity, speciation, and host adaptation of the important group of fungi.