Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes

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

Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto

“…In this study, we confirmed that the irregular distribution of MGEs does not follow divergence of cryptic species within the FGSC. This finding supports the hypothesis of low mobility of ancestrally acquired MGEs that are consequently shared by geographically diverse cryptic species ( Kulik et al, 2020b ). These ancestral elements may undergo changes throughout evolution, and assuming the lack of horizontal gene flow, these alternations should, at least in part, exhibit species-specific polymorphism.…”

“…Notably, variation in MGE content appears to be dependent on taxonomic sampling. This variation can be highly conserved, indicating a low mobility of ancestrally acquired MGEs ( Kulik et al, 2020b ). In contrast, more recent enrichment events result in increased mosaicism of MGE patterns that can be observed at the population level ( Wolters et al, 2015 ).…”

“…Comparison of mitogenomes of geographically diverse F.g. strains did not reveal any population-specific profiles, thus supporting the hypothesis on ancestral acquisition of HEGs. Assuming their early acquisition and low mobility, recently diverging cryptic species may thus share a similar content of MGEs ( Kulik et al, 2020b ). This hypothesis will be tested using mitogenomes obtained in this study.…”

“…Besides its evolutionary value, mitochondrial DNA (mtDNA) is promising in the diagnostics of fungi, especially with regard to its multi-copy nature, which facilitates its high recovery and amplification success ( Santamaria et al, 2009 ). Both MGE content variation and SNP in mitogenomes could be used for identification purposes of fusaria ( Wu et al, 2019 ; Kulik et al, 2020b ). However, discriminating cryptic species based on mitochondrial sequences is challenging due to the high degree of conservation, and detecting species-specific sites requires screening of a large set of genomic data to differentiate between intraspecific and interspecific variation ( Kulik et al, 2015 , 2020a ).…”

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

“…Linear versions have also been observed and some circular version could actually exist as linear concatemers generated by a rolling circle type DNA replication mechanism ( Bendich, 1993 ; Hausner, 2003 , 2012 ; Bullerwell and Lang, 2005 ; Baidyaroy et al, 2011 ; Valach et al, 2011 ; Chen and Clark-Walker, 2018 ). Mitochondrial genome architecture and size are highly variable among the fungi due to recombination events promoted by repeats and by the presence and activities of mobile elements such group I and group II introns and intron-encoded proteins (IEPs) ( Aguileta et al, 2014 ; Wu and Hao, 2014 , 2019 ; Franco et al, 2017 ; Repar and Warnecke, 2017 ; Deng et al, 2018 ; Stone et al, 2018 ; Zubaer et al, 2018 ; Kolesnikova et al, 2019 ; Kulik et al, 2020 ; Liu et al, 2020b ). Like other fungi, most of the mitogenome variation observed among the examined members of the Ophiostomatales is due to the absence and presence of introns.…”