Insights into the Phylogeny of Ustilago maydis Strains via Comparative Analysis of Their Respective Mitogenomes

<i>Ustilago maydis</i> is an economically significant biotrophic smut fungus, capable of infecting maize. This is a localized infection where tumors are formed, potentially in any of the aboveground parts of the plant. In extreme cases, maize plants may die. It is also dimorphic, i.e., it is capable of switching from yeast-like to filamentous forms. The switch can be induced by nitrogen sources, pH, and some lipids/oils. The active infectious form is the filamentous form which is capable of penetrating plant cells using the appressorium. This study focuses on understanding the mitochondrial genome diversity in <i>U. maydis</i>, the selection pressure on the genes encoded in the mitochondrial genome, and the phylogeny of the strains investigated. The results suggest that the strains maintained high consistency in genome architecture and synteny. The <i>cox1</i> and <i>cob</i> genes in the genomes possessed different intron numbers, with the presence or absence of homing endonuclease genes (HEGs), which overall contributed to the differences in the genome sizes. Among the genes in the mitogenome, <i>nad6</i> was the only gene that has a non-synonymous nucleotide change, but the overall changes within the mitogenomes suggest purifying selection. The study helped identify the different mitotypes using PCR, although further markers or whole-genome sequencing may be required to fully distinguish mitotypes.