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

Abstract

Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.

Whole-genome single nucleotide polymorphism analysis for typing the pandemic pathogen Fusarium graminearum sensu stricto

“…This strain is held in the fungal collection Westerdijk Fungal Biodiversity Institute (Utrecht, Netherlands) as F. graminearum and according to available metadata it was isolated from maize in South Africa where F. boothii has been frequently reported (van der Lee et al, 2015). However, our previous mitochondrial-based comprehensive studies did not indicated incorrect taxonomic status of this strain (Kulik et al, 2015;Brankovics et al, 2018;Wyre " bek et al, 2021). The complete mitogenome of CBS 119800 (NCBI accession no.…”

“…Our previous large scale sequencing project was launched in order to obtain genome sequences from a large collection of strains of the pandemic pathogen Fusarium graminearum sensu stricto ( F.g. ) ( Wyrebek et al, 2021 ). This cryptic species is mainly responsible for two cereal diseases: Fusarium Head Blight (FHB) of wheat and barley and Fusarium Ear Rot (FER) of maize.…”

“…belongs to the F. graminearum species complex (FGSC), which includes at least sixteen cryptic species ( Sarver et al, 2011 ), among them a few may be involved in cereal diseases in certain agricultural areas ( van der Lee et al, 2015 ). Determination of cryptic diversity within field populations enables us to better understand their dynamics and the evolutionary relationships underlying disease outbreaks ( van der Lee et al, 2015 ; Wyrebek et al, 2021 ). We have previously explored the value of mitochondrial sequences for diagnostic purposes of F.g. We showed that mitochondrial-based SNP analysis are useful for typing most, but not all, strains of F.g. We also underlined the limitations of clustering-based identification approaches for FGSC species using mitochondrial sequences ( Wyrebek et al, 2021 ).…”

Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients

“…Mitochondrial genomes evolve independently of and faster than the nuclear genome [10]. Mitogenomes have also been proposed as a useful tool for diagnostic purposes in Fusarium species [11]. The concept of using mitogenome diversity for the identification of species mainly derives from their higher DNA copy number compared with nuclear DNA, and hence the high recovery and amplification success in eukaryotes where insufficient phylogenetic signals have accumulated in nuclear genes [12].…”