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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.

SUBMITTER: Wyrebek J

PROVIDER: S-EPMC8439580 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Recent improvements in microbiology and molecular epidemiology were largely stimulated by whole- genome sequencing (WGS), which provides an unprecedented resolution in discriminating highly related genetic backgrounds. WGS is becoming the method of choice in epidemiology of fungal diseases, but its application is still in a pioneer stage, mainly due to the limited number of available genomes. Fungal pathogens often belong to complexes composed of numerous cryptic species. Detecting cryptic diversity is fundamental to understand the dynamics and the evolutionary relationships underlying disease outbreaks. In this study, we explore the value of whole-genome SNP analyses in identification of the pandemic pathogen Fusarium graminearum sensu stricto (F.g.). This species is responsible for cereal diseases and negatively impacts grain production worldwide. The fungus belongs to the monophyletic fungal complex referred to as F. graminearum species complex including at least sixteen cryptic species, a few among them may be involved in cereal diseases in certain agricultural areas. We analyzed WGS data from a collection of 99 F.g. strains and 33 strains representing all known cryptic species belonging to the FGSC complex. As a first step, we performed a phylogenomic analysis to reveal species-specific clustering. A RAxML maximum likelihood tree grouped all analyzed strains of F.g. into a single clade, supporting the clustering-based identification approach. Although, phylogenetic reconstructions are essential in detecting cryptic species, a phylogenomic tree does not fulfill the criteria for rapid and cost-effective approach for identification of fungi, due to the time-consuming nature of the analysis. As an alternative, analysis of WGS information by mapping sequence data from individual strains against reference genomes may provide useful markers for the rapid identification of fungi. We provide a robust framework for typing F.g. through the web-based PhaME workflow available at EDGE bioinformatics. The method was validated through multiple comparisons of assembly genomes to F.g. reference strain PH-1. We showed that the difference between intra- and interspecies variability was at least two times higher than intraspecific variation facilitating successful typing of F.g. This is the first study which employs WGS data for typing plant pathogenic fusaria.

Project description:Flavonoids are a group of hydroxylated polyphenolic compounds widely distributed in the plant kingdom. Biosynthesis of these compounds involves type III PKSs, whose presence has been recently predicted in some fungal species through genome sequencing efforts. In this study, for the first time it was found that Fusaria produce flavonoids on solid YES medium. Naringenin, as the central precursor of all flavonoids, was produced at highest quantities, followed by quercetin, kaempferol, apigenin and luteolin. In plants, flavonoids are involved in the protection of cereals to a wide range of stresses, including host defense against Fusaria. Under in vitro conditions, strains of Fusarium culmorum and F. graminearum sensu stricto were incubated at levels of flavonoids close to amounts produced by cereals in response to fungal infection. The amounts of exogenous naringenin, apigenin, luteolin, kaempferol and quercetin were reduced and converted by fungi to the other flavonoid derivatives. Treatment of fungi with naringenin derivatives led to the inhibition of naringenin production. Correspondingly, the production of fungal-derived phenolic acids decreased in flavonoid treated samples, although this effect appeared to be dependent on the strain, flavonoid molecule and its concentration. Fusaria showed high variability in trichothecene production in response to flavonoids. With emphasis on quercetin, mycotoxin accumulation in the media was significantly decreased by luteolin, kaempferol, naringenin and apigenin. However, in some cases, apigenin led to the increase of mycotoxin content in the media. Gene expression experiments of Tri genes responsible for trichothecene biosynthesis (Tri4, Tri5 and Tri10) proved that the inhibition of mycotoxin production by flavonoids occurred at the transcriptional level. However, the changes in Tri transcript levels were not significant in most apigenin and all kaempferol-treated cultures. In this study, a link was established between antioxidant and antiradical properties of flavonoids and their effects on fungi.

Project description:BackgroundThe Commerson's leaf-nosed bat, Hipposideros commersoni sensu stricto, is endemic to Madagascar and is relatively common in the western portion of the island, where it is found in areas, including forested zones, from sea level to 1325 m. A previous study on morphological patterns of geographic variation within the species highlighted the presence of two distinct morphotypes; larger individuals in the north portion of the island and smaller individuals in the south. The main aim of this study was to use a combination of craniodental morphology and molecular data (mitochondrial and nuclear) to test previous hypotheses based on morphology and clarify the evolutionary history of the species group.MethodsWe sequenced mitochondrial and nuclear genes from Hipposideros commersoni obtained from the western portion of Madagascar, and compared them with other African species as outgroups. We analyzed the sequence data using Maximum Likelihood and Bayesian phylogenetic inference. Divergence dates were estimated using Bayesian molecular clock approach. Variation in craniodental variables was also assessed from sequenced individuals.ResultsThe molecular analyses suggest that H. commersoni is not monophyletic, with strong support for the presence of several independently evolving lineages. Two individuals amongst those sequenced from Isalo (south central) and Itampolo (southwest) form a separate clade (Clade A), distinct from other H. commersoni, and sister to continental African H. vittatus and H. gigas. Within the H. commersoni clade, the molecular data support two geographically distributed clades; one from the south (Clade B) and the other from the north (Clade C), which diverged approximately 3.38 million years ago. Morphometric data were consistent with the molecular analyses, suggesting a north-south break within H. commersoni. However, at some localities, animals from both clades occurred in sympatry and these individuals could not be differentiated based on external and craniodental measurements.ConclusionsUsing a combination of molecular and morphological characters, this study presents evidence of cryptic diversity in H. commersoni on Madagascar. Further fine-scale phylogeographic studies are needed to fully resolve the systematics of H. commersoni. This study highlights the utility of the combined approach in employing both morphological and molecular data to provide insights into the evolutionary history of Malagasy population currently assigned to H. commersoni.

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

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