Return of the mitochondrial DNA Case study of mitochondrial genome evolution in the genus Fusarium

Mitochondrial DNA played a prominent role in the fields of population genetics, systematics and evolutionary biology, due to its favorable characteristics, such as, uniparental inheritance, fast evolution and easy accessibility. However, the mitochondrial sequences have been mostly neglected in fungi since the initiation of the barcoding of life project, due to technical difficulties. This shifted the focus in fungal systematics and phylogenetics from the mitochondrion to the nuclear rDNA repeat region and single copy nuclear housekeeping genes. The combination of whole genome sequencing and new bioinformatics software, such as GRAbB (introduced in this thesis), overcome these difficulties, and pave the way for large scale comparative mitochondrial genomics as an important part of evolutionary studies.
The work presented in this thesis demonstrates that large numbers of strains can be compared for a specific region (the mitogenome in our case) by using the selective assembly approach, that introns and homing endonuclease genes play an important role in the mitochondrial genome evolution, and that comparative mitochondrial genome analysis can lead to new insights into our understanding of the biology and evolutionary history of the organism. Such insights are the cryptic sexual or parasexual cycle in F. oxysproum, and that horizontal transfer has played an important role in the evolutionary history of F. fujikuroi & F. oxysporum species complexes, which should be taken into consideration when studying individual gene genealogies within these groups.