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

Joanna Wyrębek,Tomasz Molcan,Anne D Van Diepeningen,Tomasz Kulik,Maciej Żelechowski,Alexander A Stakheev,Kamil Myszczyński,Katarzyna Bilska

doi:10.3389/fmicb.2021.714651

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.

Highlights

Fusarium graminearum sensu stricto (F.g.) ranks number 4 in the top 10 most important and best-studied species that cause diseases on agriculturally important plants (Dean et al, 2012)
122 strains were analyzed in this study, with 88 F.g. strains and 34 strains representing all known cryptic species from the F. graminearum species complex (FGSC) complex: Fusarium acaciae-mearnsii, Fusarium aethiopicum, Fusarium asiaticum, Fusarium austroamericanum, Fusarium boothii, Fusarium brasilicum, Fusarium cortadariae, Fusarium gerlachii, Fusarium louisianense, Fusarium meridionale, F. meridionale × F. asiaticum hybrid strain, Fusarium mesoamericanum, Fusarium nepalense, Fusarium ussurianum, Fusarium vorosii, and strain CBS 123663, which lacks a Latin binomial
Mitogenomes of species within the FGSC are highly conserved in terms of a set of 15 protein-coding genes, two rRNA genes, and 28 tRNA genes, which were localized in the same order and orientation

Summary

Introduction

Fusarium graminearum sensu stricto (F.g.) ranks number 4 in the top 10 most important and best-studied species that cause diseases on agriculturally important plants (Dean et al, 2012). F.g. belongs to the monophyletic fungal complex referred to as F. graminearum species complex (FGSC) This complex includes 16 genetically characterized cryptic species (Sarver et al, 2011), several of which are involved in cereal diseases in certain agricultural areas. The species are difficult to identify by morphological characters and often share a high DNA sequence similarity (Walkowiak et al, 2016) Despite their close relationship, FGSC species and even strains within species can exhibit distinct phenotypic differences in pathogenicity and mycotoxin production, while some strains lack pathogenicity on certain hosts (Jianbo, 2014; van der Lee et al, 2015; Walkowiak et al, 2016)

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