Dataset Information

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 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.

SUBMITTER: Kulik T

PROVIDER: S-EPMC7263005 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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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.

Kulik Tomasz T Brankovics Balazs B van Diepeningen Anne D AD Bilska Katarzyna K Żelechowski Maciej M Myszczyński Kamil K Molcan Tomasz T Stakheev Alexander A Stenglein Sebastian S Beyer Marco M Pasquali Matias M Sawicki Jakub J Wyrȩbek Joanna J Baturo-Cieśniewska Anna A

Frontiers in microbiology 20200525

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 fu ...[more]

PMID: 32528440

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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:There is a gradual shift from representing a species' genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The "intronless" mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the "host" gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

Dataset Information

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.

Publications

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

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