Abstract
Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.
Highlights
Most fungi contain mitochondria, organelles playing a key role in the generation of metabolic energy
This study demonstrates that the variable landscape of mobile genetic elements (MGEs) is the most prominent type of variation among mitogenomes of closely related F. graminearum s.s. and F. culmorum
F. graminearum s.s. did not harbor unique MGEs throughout the mitogenome, we found that MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L that can serve as potential markers for the identification of this species
Summary
Organelles playing a key role in the generation of metabolic energy. Fungal mitochondria have been shown to contribute to diverse cellular and organismal functions including senescence, quiescence, biofilm regulation and hyphal growth (Chatre and Ricchetti, 2014; Calderone et al, 2015; Bartelli et al, 2018; Sandor et al, 2018). Mitogenomes are expected to provide new insights for understanding the phylogenetic relationships and evolutionary biology of fungi (Aguileta et al, 2014; Lin et al, 2015; Franco et al, 2017) The reason for this is that fungal mitogenomes are highly divergent among even closely related lineages (Yin et al, 2012; Pogoda et al, 2019). For many fungal lineages, the characterization of mitochondrial DNA (mtDNA) has been largely limited by a low number of mitochondrial sequences in the GenBank database
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